Variant report

Variant	rs12258965
Chromosome Location	chr10:531982-531983
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10128217	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10128281	1.00[JPT][hapmap]
rs10128312	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11252756	1.00[CEU][hapmap];0.85[GIH][hapmap]
rs11252772	1.00[CEU][hapmap]
rs11252791	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[TSI][hapmap]
rs11252809	1.00[CEU][hapmap]
rs11253065	0.88[CHD][hapmap];0.87[ASN][1000 genomes]
rs11253258	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11253259	1.00[CEU][hapmap]
rs11253265	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12245224	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs12246490	0.90[ASN][1000 genomes]
rs12249596	1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs12251997	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[TSI][hapmap];0.97[ASN][1000 genomes]
rs12255922	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12261462	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12263280	0.94[ASN][1000 genomes]
rs12265644	1.00[JPT][hapmap]
rs12267607	0.94[ASN][1000 genomes]
rs1539231	1.00[CEU][hapmap]
rs1672534	1.00[CEU][hapmap]
rs17136375	0.88[CHD][hapmap]
rs17159676	1.00[JPT][hapmap]
rs17159691	1.00[CEU][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs17159711	1.00[CEU][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs17159715	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs17159756	0.88[CHD][hapmap]
rs1773487	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2096134	0.85[GIH][hapmap]
rs2386709	0.87[CHD][hapmap]
rs4472852	1.00[JPT][hapmap]
rs4881337	1.00[CEU][hapmap]
rs4881345	1.00[CEU][hapmap]
rs73576221	0.81[ASN][1000 genomes]
rs73577727	0.87[ASN][1000 genomes]
rs73581612	0.94[ASN][1000 genomes]
rs7912391	0.83[CHD][hapmap]
rs816600	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[ASN][1000 genomes]
rs816650	0.83[CHD][hapmap]
rs885593	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[TSI][hapmap];0.87[ASN][1000 genomes]
rs947469	1.00[CEU][hapmap];0.84[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:39 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531919	chr10:60001-668649	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1042404	chr10:224406-567104	Genic enhancers Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv540381	chr10:224406-567104	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1046313	chr10:224406-691123	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv540385	chr10:224406-691123	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv1036501	chr10:224406-775824	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv1052660	chr10:224406-785929	Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv1043752	chr10:224406-789665	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv916363	chr10:224406-816628	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
10	nsv916591	chr10:224406-1088734	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
11	nsv540386	chr10:224406-1197416	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
12	nsv530114	chr10:226083-596534	ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
13	nsv1035580	chr10:248463-832240	Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
14	nsv540392	chr10:248463-832240	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
15	nsv466693	chr10:255222-566195	Weak transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
16	nsv549750	chr10:255222-566195	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
17	nsv1040466	chr10:278544-626866	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
18	nsv932647	chr10:278852-624284	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
19	nsv530115	chr10:294172-633529	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
20	nsv549751	chr10:313304-734229	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
21	nsv1048957	chr10:375035-556244	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
22	nsv540396	chr10:375035-556244	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
23	nsv1050252	chr10:375035-839594	Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
24	nsv540397	chr10:375035-839594	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
25	nsv1036348	chr10:387880-817037	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
26	nsv894704	chr10:393676-565362	Bivalent Enhancer Strong transcription Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
27	nsv894705	chr10:399104-565362	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
28	nsv1051016	chr10:419265-647337	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
29	nsv540398	chr10:419265-647337	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
30	nsv428798	chr10:421999-582579	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
31	nsv1035712	chr10:436747-714987	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
32	nsv1048859	chr10:442805-887622	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
33	nsv1039958	chr10:450753-889167	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
34	nsv540400	chr10:450753-889167	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
35	nsv549753	chr10:458477-894838	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
36	nsv831765	chr10:466002-631099	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
37	nsv540401	chr10:484201-556959	Strong transcription Bivalent Enhancer Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
38	nsv868946	chr10:503401-816628	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
39	nsv894706	chr10:518199-583548	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12258965	MEST	trans	lymphoblastoid	seeQTL

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:517000-536800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr10:523000-532600	Weak transcription	Spleen	Spleen
3	chr10:524400-532400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr10:526200-532600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr10:530000-533400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr10:530200-532000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr10:530400-532600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr10:530600-536000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr10:531000-532000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
10	chr10:531000-532600	Flanking Active TSS	Stomach Smooth Muscle	stomach
11	chr10:531000-533200	Enhancers	Fetal Heart	heart
12	chr10:531000-533600	Enhancers	Fetal Brain Male	brain
13	chr10:531200-532000	Genic enhancers	Fetal Muscle Leg	muscle
14	chr10:531200-532400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr10:531200-532800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
16	chr10:531200-532800	Strong transcription	Fetal Intestine Small	intestine
17	chr10:531200-533000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr10:531200-533400	Enhancers	Brain Germinal Matrix	brain
19	chr10:531200-536200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr10:531200-536200	Weak transcription	Placenta	Placenta
21	chr10:531200-536800	Weak transcription	Fetal Intestine Large	intestine
22	chr10:531400-532000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr10:531400-532000	Enhancers	Primary B cells from peripheral blood	blood
24	chr10:531400-532000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr10:531400-532000	Enhancers	Pancreas	Pancrea
26	chr10:531400-532000	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr10:531400-532000	Enhancers	Right Ventricle	heart
28	chr10:531400-532000	Enhancers	HUVEC	blood vessel
29	chr10:531400-532200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr10:531400-532400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr10:531400-532400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr10:531400-532400	Enhancers	Left Ventricle	heart
33	chr10:531400-532600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr10:531400-532800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
35	chr10:531400-532800	Enhancers	Fetal Lung	lung
36	chr10:531400-533000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr10:531400-533000	Enhancers	Fetal Muscle Trunk	muscle
38	chr10:531400-533200	Enhancers	H1 Cell Line	embryonic stem cell
39	chr10:531400-533200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr10:531400-533200	Enhancers	Fetal Brain Female	brain
41	chr10:531400-533400	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr10:531400-533400	Enhancers	Rectal Smooth Muscle	rectum
43	chr10:531400-533600	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr10:531400-534200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr10:531400-534400	Weak transcription	Lung	lung
46	chr10:531400-534600	Weak transcription	Aorta	Aorta
47	chr10:531400-534600	Weak transcription	Right Atrium	heart
48	chr10:531400-535600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr10:531400-536200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr10:531400-536200	Weak transcription	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links