Variant report

Variant	rs2107613
Chromosome Location	chr12:888428-888429
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF384	chr12:888392-888651	GM12878	blood:	n/a	n/a
2	MYC	chr12:888247-888434	MCF10A-Er-Src	breast:	n/a	n/a
3	E2F4	chr12:888299-888429	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
RNU4ATAC16P	TF binding region

Extended variants
information (count: 91 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1012729	0.81[CEU][hapmap]
rs1051669	0.81[CEU][hapmap]
rs10735063	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10735064	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10735065	0.80[ASN][1000 genomes]
rs10774459	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10774463	0.87[ASN][1000 genomes]
rs10774464	0.86[JPT][hapmap]
rs10774466	0.80[ASN][1000 genomes]
rs10849559	0.86[JPT][hapmap]
rs10849563	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10849568	0.80[ASN][1000 genomes]
rs11064519	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs11064560	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11571430	0.86[CEU][hapmap]
rs1159744	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11608756	0.86[JPT][hapmap]
rs11832907	0.80[CEU][hapmap]
rs1970996	0.80[ASN][1000 genomes]
rs2014160	0.87[ASN][1000 genomes]
rs2107612	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2107614	0.87[ASN][1000 genomes]
rs2158502	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2240282	0.80[ASN][1000 genomes]
rs2240283	0.80[ASN][1000 genomes]
rs2286007	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs2301880	0.85[CEU][hapmap]
rs2369402	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2369490	0.84[ASN][1000 genomes]
rs2369491	0.80[ASN][1000 genomes]
rs3858703	0.86[CHB][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs4388955	0.80[ASN][1000 genomes]
rs4766377	0.81[CEU][hapmap]
rs4980968	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4980969	0.80[ASN][1000 genomes]
rs4980970	0.80[ASN][1000 genomes]
rs6489746	0.89[ASW][hapmap];0.95[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6489749	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6489752	0.84[CEU][hapmap];0.80[ASN][1000 genomes]
rs6489754	0.80[ASN][1000 genomes]
rs6489757	0.80[ASN][1000 genomes]
rs67969314	0.83[ASN][1000 genomes]
rs724709	0.87[ASN][1000 genomes]
rs7295704	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7298001	0.80[ASN][1000 genomes]
rs7300056	0.80[ASN][1000 genomes]
rs7301349	0.80[ASN][1000 genomes]
rs7311065	0.87[ASN][1000 genomes]
rs7311423	0.80[ASN][1000 genomes]
rs765250	1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7959921	0.80[ASN][1000 genomes]
rs7966632	0.87[ASN][1000 genomes]
rs7971329	0.80[ASN][1000 genomes]
rs7972490	0.85[CEU][hapmap]
rs7972667	0.86[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs7980163	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:35 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv541305	chr12:282465-1016828	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv869390	chr12:282465-1045994	Strong transcription Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv1049944	chr12:282465-1232077	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS 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	80 gene(s)	inside rSNPs	diseases
4	nsv541306	chr12:282465-1232077	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats 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 target site	80 gene(s)	inside rSNPs	diseases
5	nsv1044433	chr12:321619-1065402	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
6	nsv541323	chr12:321619-1065402	Strong transcription Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
7	esv2759875	chr12:335010-990544	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
8	nsv1045638	chr12:349031-893536	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
9	nsv541325	chr12:349031-893536	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
10	nsv949469	chr12:380411-1122450	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
11	esv2758290	chr12:457433-990544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
12	nsv898568	chr12:547683-969800	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
13	nsv556890	chr12:662448-1100555	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
14	nsv556892	chr12:673515-1210884	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
15	nsv1051590	chr12:722215-974773	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
16	nsv541338	chr12:722215-974773	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription 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	26 gene(s)	inside rSNPs	diseases
17	nsv468956	chr12:737230-982321	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS 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	26 gene(s)	inside rSNPs	diseases
18	nsv556893	chr12:737230-982321	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
19	esv2757485	chr12:786238-964551	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
20	nsv1046707	chr12:792110-910520	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
21	nsv898576	chr12:813411-1553450	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
22	esv2754685	chr12:835074-936468	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
23	esv2753750	chr12:835074-939480	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
24	esv2753658	chr12:835074-964506	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
25	esv3693103	chr12:837113-971317	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
26	nsv556898	chr12:850288-968489	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
27	nsv468959	chr12:850613-922408	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
28	nsv556899	chr12:850613-922408	Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
29	nsv518946	chr12:854331-961336	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
30	nsv556900	chr12:854331-968489	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
31	esv2752382	chr12:863833-964506	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
32	nsv948760	chr12:863833-1542875	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
33	esv1840640	chr12:866857-898400	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
34	nsv898577	chr12:873890-969800	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
35	nsv898578	chr12:876288-909731	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2107613	ITPKB	trans	lymphoblastoid	seeQTL
rs2107613	RAD52	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:865200-895600	Weak transcription	Pancreas	Pancrea
2	chr12:866000-889200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr12:866400-888800	Weak transcription	HMEC	breast
4	chr12:866800-888800	Weak transcription	Fetal Intestine Large	intestine
5	chr12:871000-888800	Weak transcription	NH-A	brain
6	chr12:872600-889600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr12:873200-889000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:877600-888800	Weak transcription	Fetal Muscle Leg	muscle
9	chr12:879200-889800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr12:881800-889200	Weak transcription	Duodenum Mucosa	Duodenum
11	chr12:881800-891400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr12:883400-889000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr12:883400-889000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr12:883600-888800	Weak transcription	HSMMtube	muscle
15	chr12:883600-889000	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr12:883600-889200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr12:883600-889400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr12:883600-905200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr12:883800-888600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr12:883800-923200	Weak transcription	Fetal Stomach	stomach
21	chr12:884000-888600	Weak transcription	HSMM	muscle
22	chr12:884000-888800	Weak transcription	Fetal Lung	lung
23	chr12:884000-891600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr12:884600-888800	Enhancers	Primary T cells fromperipheralblood	blood
25	chr12:884800-888800	Weak transcription	Right Atrium	heart
26	chr12:884800-891600	Enhancers	Brain Hippocampus Middle	brain
27	chr12:884800-899000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr12:885000-888800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr12:885000-889600	Weak transcription	Right Ventricle	heart
30	chr12:885200-888600	Weak transcription	Adipose Nuclei	Adipose
31	chr12:885200-890600	Enhancers	Brain Substantia Nigra	brain
32	chr12:885200-896000	Weak transcription	Dnd41	blood
33	chr12:885400-888600	Weak transcription	Aorta	Aorta
34	chr12:885400-888600	Weak transcription	Psoas Muscle	Psoas
35	chr12:885400-889600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr12:885400-891800	Weak transcription	Fetal Thymus	thymus
37	chr12:885400-897000	Weak transcription	Fetal Intestine Small	intestine
38	chr12:885400-898400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr12:885400-904000	Weak transcription	Thymus	Thymus
40	chr12:885600-889000	Weak transcription	Brain Cingulate Gyrus	brain
41	chr12:885600-890000	Enhancers	Stomach Mucosa	stomach
42	chr12:885600-892000	Weak transcription	Ovary	ovary
43	chr12:886000-888800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr12:886000-895800	Weak transcription	Lung	lung
45	chr12:886200-890600	Enhancers	Colon Smooth Muscle	Colon
46	chr12:886200-891600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr12:886400-888800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr12:886600-888600	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr12:886600-890000	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr12:886600-891400	Enhancers	Primary T helper naive cells from peripheral blood	blood

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