Variant report

Variant	rs7952938
Chromosome Location	chr12:49934011-49934012
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SUZ12	chr12:49933283-49934929	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49930852..49937653-chr12:49953841..49959391,7	K562	blood:
2	chr12:49759353..49761548-chr12:49931777..49934189,4	K562	blood:
3	chr12:49930865..49935032-chr12:49959689..49963246,5	K562	blood:
4	chr12:49933783..49936509-chr12:49951821..49953726,3	K562	blood:
5	chr12:49931420..49936579-chr12:49960006..49963071,6	MCF-7	breast:
6	chr12:49657699..49660591-chr12:49932809..49935394,2	MCF-7	breast:

No data

Variant related genes	Relation type
KCNH3	TF binding region
ENSG00000123352	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000110844	Chromatin interaction
ENSG00000187778	Chromatin interaction
ENSG00000167553	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs11169043	0.84[ASN][1000 genomes]
rs11169045	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11169063	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11169065	0.86[ASN][1000 genomes]
rs11169069	0.86[ASN][1000 genomes]
rs11169070	0.81[ASN][1000 genomes]
rs11169073	0.86[ASN][1000 genomes]
rs11169076	0.86[ASN][1000 genomes]
rs11169080	0.97[ASN][1000 genomes]
rs11169081	0.86[ASN][1000 genomes]
rs11169082	0.86[ASN][1000 genomes]
rs11169092	0.81[ASN][1000 genomes]
rs11169097	0.81[ASN][1000 genomes]
rs11169101	0.82[ASN][1000 genomes]
rs1150057	0.86[ASN][1000 genomes]
rs11615710	0.84[ASN][1000 genomes]
rs11833411	0.81[ASN][1000 genomes]
rs12299505	0.81[ASN][1000 genomes]
rs12299513	0.81[ASN][1000 genomes]
rs12311527	0.86[ASN][1000 genomes]
rs12311839	0.86[ASN][1000 genomes]
rs12314878	0.86[ASN][1000 genomes]
rs12320556	0.86[ASN][1000 genomes]
rs12321819	0.86[ASN][1000 genomes]
rs13066	0.86[ASN][1000 genomes]
rs13906	0.86[ASN][1000 genomes]
rs17123808	0.86[ASN][1000 genomes]
rs1902329	0.86[ASN][1000 genomes]
rs1902330	0.86[ASN][1000 genomes]
rs2005195	0.86[ASN][1000 genomes]
rs2241418	0.86[ASN][1000 genomes]
rs2278068	0.86[ASN][1000 genomes]
rs2278069	0.86[ASN][1000 genomes]
rs2278070	0.84[ASN][1000 genomes]
rs2303305	0.84[ASN][1000 genomes]
rs2878532	0.92[ASN][1000 genomes]
rs3815832	0.86[ASN][1000 genomes]
rs3887727	0.97[ASN][1000 genomes]
rs3887728	0.86[ASN][1000 genomes]
rs4045193	0.81[ASN][1000 genomes]
rs4073998	0.89[ASN][1000 genomes]
rs52824916	0.84[ASN][1000 genomes]
rs55853522	0.86[ASN][1000 genomes]
rs57916875	0.84[ASN][1000 genomes]
rs58125498	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs59940006	0.86[ASN][1000 genomes]
rs61512987	0.92[ASN][1000 genomes]
rs61616163	0.82[ASN][1000 genomes]
rs7131915	0.86[ASN][1000 genomes]
rs7132792	0.86[ASN][1000 genomes]
rs7295556	0.84[ASN][1000 genomes]
rs7296281	0.86[ASN][1000 genomes]
rs7301209	0.86[ASN][1000 genomes]
rs73305008	0.86[ASN][1000 genomes]
rs73305012	0.86[ASN][1000 genomes]
rs7953911	0.86[ASN][1000 genomes]
rs7962863	0.82[ASN][1000 genomes]
rs7963954	0.82[ASN][1000 genomes]
rs7965658	0.89[ASN][1000 genomes]
rs7970241	0.86[ASN][1000 genomes]
rs7973389	0.86[ASN][1000 genomes]
rs7975599	0.86[ASN][1000 genomes]
rs7975712	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7977389	0.86[ASN][1000 genomes]
rs7979285	0.97[ASN][1000 genomes]
rs8626	0.92[ASN][1000 genomes]
rs876889	0.84[ASN][1000 genomes]
rs933738	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899070	chr12:49811311-49941500	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv832406	chr12:49860693-50062136	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv482795	chr12:49897633-50068686	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv1801776	chr12:49915354-49934565	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv899071	chr12:49927148-49955935	Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv3431223	chr12:49931235-49934833	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49931200-49935000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr12:49931800-49934200	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr12:49932800-49934200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr12:49932800-49934200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr12:49932800-49934200	Bivalent Enhancer	Fetal Muscle Leg	muscle
6	chr12:49932800-49934200	Bivalent Enhancer	Placenta	Placenta
7	chr12:49932800-49935400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
8	chr12:49933000-49942600	Weak transcription	Pancreas	Pancrea
9	chr12:49933200-49934200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr12:49933200-49934200	Bivalent Enhancer	Fetal Thymus	thymus
11	chr12:49933200-49934400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
12	chr12:49933400-49934200	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:49933400-49934200	Bivalent Enhancer	Fetal Lung	lung
14	chr12:49933400-49934200	Bivalent Enhancer	GM12878-XiMat	blood
15	chr12:49933400-49934400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr12:49933400-49934600	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
17	chr12:49933400-49934800	Bivalent Enhancer	Fetal Intestine Large	intestine
18	chr12:49933400-49934800	Bivalent Enhancer	Fetal Intestine Small	intestine
19	chr12:49933400-49935000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr12:49933400-49935400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
21	chr12:49933400-49942000	Weak transcription	Right Ventricle	heart
22	chr12:49933400-49942400	Weak transcription	Right Atrium	heart
23	chr12:49933600-49934200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr12:49933600-49934200	Bivalent Enhancer	Brain Germinal Matrix	brain
25	chr12:49933600-49934200	Bivalent Enhancer	Fetal Brain Male	brain
26	chr12:49933600-49934400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
27	chr12:49933600-49934400	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr12:49933600-49934600	Enhancers	A549	lung
29	chr12:49933600-49934800	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr12:49933600-49934800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr12:49933600-49935200	Enhancers	HMEC	breast
32	chr12:49933600-49935400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr12:49933600-49935800	Enhancers	Primary B cells from cord blood	blood
34	chr12:49933600-49937600	Weak transcription	Ovary	ovary
35	chr12:49933800-49934200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
36	chr12:49933800-49934200	Bivalent Enhancer	Primary T cells from cord blood	blood
37	chr12:49933800-49934200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr12:49933800-49934200	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
39	chr12:49933800-49934600	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr12:49933800-49935000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
41	chr12:49933800-49935200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
42	chr12:49934000-49934200	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr12:49934000-49934200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
44	chr12:49934000-49934200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr12:49934000-49934200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr12:49934000-49934200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
47	chr12:49934000-49934400	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
48	chr12:49934000-49934400	Bivalent Enhancer	HepG2	liver
49	chr12:49934000-49934400	Flanking Active TSS	NHEK	skin
50	chr12:49934000-49934600	Active TSS	Brain Angular Gyrus	brain

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