Variant report

Variant	rs7961416
Chromosome Location	chr12:9804413-9804414
allele	C/G
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	MTA3	chr12:9799406-9804477	GM12878	blood:	n/a	n/a
2	RELA	chr12:9803312-9804472	GM18526	blood:	n/a	n/a
3	POLR2A	chr12:9799501-9804451	GM12891	blood:	n/a	n/a
4	POLR2A	chr12:9799328-9804610	GM12878	blood:	n/a	n/a
5	ATF2	chr12:9800087-9804473	GM12878	blood:	n/a	n/a
6	CBX3	chr12:9803724-9804484	K562	blood:	n/a	n/a
7	POLR2A	chr12:9799314-9804469	GM12892	blood:	n/a	n/a
8	RELA	chr12:9803258-9804469	GM10847	blood:	n/a	n/a
9	POLR2A	chr12:9799501-9804422	GM18526	blood:	n/a	n/a
10	RELA	chr12:9799625-9804451	GM19193	blood:	n/a	n/a
11	GATA2	chr12:9804121-9804421	K562	blood:	n/a	n/a
12	RUNX3	chr12:9803209-9804465	GM12878	blood:	n/a	chr12:9803476-9803491
13	MTA3	chr12:9803869-9804581	GM12878	blood:	n/a	n/a
14	RELA	chr12:9799841-9804488	GM18951	blood:	n/a	n/a
15	POLR2A	chr12:9799520-9804579	GM12878	blood:	n/a	n/a
16	RUNX3	chr12:9802733-9804441	GM12878	blood:	n/a	chr12:9803476-9803491
17	POLR2A	chr12:9799348-9804458	GM12892	blood:	n/a	n/a
18	SPI1	chr12:9803287-9804532	HL-60	blood:	n/a	n/a
19	PML	chr12:9800165-9804429	GM12878	blood:	n/a	chr12:9800521-9800529 chr12:9802383-9802391
20	KAP1	chr12:9804342-9804859	K562	blood:	n/a	n/a
21	POLR2A	chr12:9804386-9804431	K562	blood:	n/a	n/a
22	ZBTB33	chr12:9803937-9804428	GM12878	blood:	n/a	n/a
23	POLR2A	chr12:9803761-9804455	HL-60	blood:	n/a	n/a
24	BHLHE40	chr12:9803246-9804557	GM12878	blood:	n/a	n/a
25	ARID3A	chr12:9804161-9804548	K562	blood:	n/a	n/a
26	POLR2A	chr12:9803242-9804534	HL-60	blood:	n/a	n/a
27	POLR2A	chr12:9799685-9804489	GM12892	blood:	n/a	n/a
28	POLR2A	chr12:9799380-9804524	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:9798786..9803516-chr12:9803864..9807970,10	MCF-7	breast:
2	chr12:9802928..9804462-chr12:9806298..9808980,2	K562	blood:
3	chr12:9800783..9805047-chr12:9809567..9813940,5	K562	blood:
4	chr12:9799323..9802837-chr12:9803671..9808302,9	K562	blood:

Variant related genes	Relation type
ENSG00000256442	TF binding region
ENSG00000256594	TF binding region
ENSG00000256442	Chromatin interaction
ENSG00000257027	Chromatin interaction
ENSG00000256594	Chromatin interaction

Extended variants
information (count: 119 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs1008611	1.00[JPT][hapmap]
rs10466762	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10743820	1.00[JPT][hapmap]
rs10743822	1.00[JPT][hapmap]
rs10772005	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10772006	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10772104	1.00[JPT][hapmap]
rs10772119	1.00[JPT][hapmap]
rs10772120	1.00[JPT][hapmap]
rs10844236	0.82[CEU][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10844267	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10844327	1.00[ASN][1000 genomes]
rs10844350	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10844351	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10844352	1.00[ASN][1000 genomes]
rs10844353	1.00[ASN][1000 genomes]
rs10844359	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10844369	0.89[ASN][1000 genomes]
rs10844372	1.00[JPT][hapmap]
rs10844418	1.00[JPT][hapmap]
rs10844424	1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap]
rs10844429	1.00[JPT][hapmap]
rs10844780	1.00[JPT][hapmap]
rs11052207	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052209	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052234	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052235	1.00[ASN][1000 genomes]
rs11052241	1.00[JPT][hapmap]
rs11052245	1.00[ASN][1000 genomes]
rs11052254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052282	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052430	1.00[JPT][hapmap]
rs11053051	1.00[JPT][hapmap]
rs11608817	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12310789	1.00[ASN][1000 genomes]
rs12366653	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12366792	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12368445	1.00[JPT][hapmap]
rs12578928	1.00[JPT][hapmap]
rs12809846	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12810851	1.00[JPT][hapmap]
rs12820641	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12823699	1.00[JPT][hapmap]
rs12824491	1.00[JPT][hapmap]
rs12825507	1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap]
rs12828602	1.00[JPT][hapmap]
rs12830419	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12831287	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12831453	1.00[JPT][hapmap]
rs1560008	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16913477	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1863871	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1990533	1.00[JPT][hapmap]
rs2114869	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2114872	1.00[JPT][hapmap]
rs2162657	1.00[ASN][1000 genomes]
rs2401396	1.00[JPT][hapmap]
rs2401397	1.00[JPT][hapmap]
rs2401398	1.00[JPT][hapmap]
rs3176800	1.00[JPT][hapmap]
rs3176802	1.00[JPT][hapmap]
rs3176806	1.00[JPT][hapmap]
rs34323946	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34833649	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34981673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35015427	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35098654	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35181877	0.89[ASN][1000 genomes]
rs35280686	1.00[ASN][1000 genomes]
rs35561167	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35642909	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35671537	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35884213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55873283	1.00[ASN][1000 genomes]
rs61916061	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6416258	1.00[JPT][hapmap]
rs6488065	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs704223	1.00[JPT][hapmap]
rs7132037	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7136821	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7299738	1.00[ASN][1000 genomes]
rs7302110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7302746	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7303246	0.89[ASN][1000 genomes]
rs7304321	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7304464	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7305937	1.00[ASN][1000 genomes]
rs7309800	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7310405	1.00[ASN][1000 genomes]
rs7310516	1.00[ASN][1000 genomes]
rs7310568	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7310790	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7310897	1.00[JPT][hapmap]
rs7311421	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7311574	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7311945	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7312624	1.00[JPT][hapmap]
rs7959406	1.00[ASN][1000 genomes]
rs7959726	1.00[ASN][1000 genomes]
rs7961262	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7962321	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7967102	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7973603	1.00[ASN][1000 genomes]
rs7974871	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7978187	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs929615	1.00[JPT][hapmap]
rs958340	1.00[ASN][1000 genomes]
rs9630265	1.00[JPT][hapmap]
rs982511	1.00[JPT][hapmap]
rs9919786	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9919787	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427903	chr12:9371593-9830668	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
4	esv1821732	chr12:9560087-9830668	Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv1823760	chr12:9560087-9830668	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv428271	chr12:9560087-9830668	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	esv2757489	chr12:9583455-9810764	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv917178	chr12:9637315-9820153	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7961416	RP11-705C15.3	cis	Whole Blood	GTEx
rs7961416	RP11-705C15.3	cis	Skin Sun Exposed Lower leg	GTEx
rs7961416	GABARAPL1	cis	parietal	SCAN
rs7961416	CLEC2D	cis	Thyroid	GTEx
rs7961416	PRB4	cis	parietal	SCAN
rs7961416	DCAL1	cis	multi-tissue	Pritchard
rs7961416	CLEC2D	cis	Esophagus Muscularis	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9801600-9811200	Weak transcription	Gastric	stomach
2	chr12:9801600-9815600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:9802000-9805200	Flanking Active TSS	Dnd41	blood
4	chr12:9802200-9806600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr12:9802200-9815200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr12:9802400-9806200	Weak transcription	A549	lung
7	chr12:9802400-9849800	Weak transcription	Pancreas	Pancrea
8	chr12:9802600-9807200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr12:9802600-9812800	Weak transcription	Ovary	ovary
10	chr12:9802600-9814400	Weak transcription	Colon Smooth Muscle	Colon
11	chr12:9803000-9804600	Flanking Active TSS	GM12878-XiMat	blood
12	chr12:9803000-9805000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:9803000-9806000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr12:9803000-9806600	Weak transcription	Placenta	Placenta
15	chr12:9803000-9806600	Weak transcription	Psoas Muscle	Psoas
16	chr12:9803000-9811200	Weak transcription	Fetal Intestine Small	intestine
17	chr12:9803000-9812200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr12:9803000-9816400	Weak transcription	Brain Germinal Matrix	brain
19	chr12:9803000-9816800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr12:9803000-9819800	Weak transcription	Fetal Brain Female	brain
21	chr12:9803000-9820200	Weak transcription	Brain Substantia Nigra	brain
22	chr12:9803000-9822200	Weak transcription	Small Intestine	intestine
23	chr12:9803200-9812400	Weak transcription	Liver	Liver
24	chr12:9803200-9813400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr12:9803400-9804600	Enhancers	HMEC	breast
26	chr12:9803400-9804600	Enhancers	HSMM	muscle
27	chr12:9803400-9806200	Weak transcription	Fetal Muscle Trunk	muscle
28	chr12:9803600-9804600	Enhancers	NHEK	skin
29	chr12:9803600-9804800	Enhancers	Primary hematopoietic stem cells	blood
30	chr12:9803600-9804800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
31	chr12:9803600-9805000	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr12:9803600-9805200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
33	chr12:9803600-9806000	Weak transcription	Fetal Intestine Large	intestine
34	chr12:9803600-9806400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
35	chr12:9803600-9806600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr12:9803600-9806800	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr12:9803600-9812200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr12:9803600-9826200	Weak transcription	Esophagus	oesophagus
39	chr12:9803800-9805600	Enhancers	HepG2	liver
40	chr12:9803800-9806200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr12:9803800-9806200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
42	chr12:9803800-9806600	Weak transcription	Adipose Nuclei	Adipose
43	chr12:9804000-9804600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr12:9804000-9805200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr12:9804000-9806000	Enhancers	Primary B cells from peripheral blood	blood
46	chr12:9804000-9806200	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr12:9804000-9806800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr12:9804000-9806800	Weak transcription	Rectal Smooth Muscle	rectum
49	chr12:9804000-9814200	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr12:9804200-9804600	Active TSS	Primary T regulatory cells fromperipheralblood	blood

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