Variant report

Variant	rs7965829
Chromosome Location	chr12:120507223-120507224
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	HNF4A	chr12:120507136-120507386	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:120504846..120507314-chr12:120512552..120515241,2	MCF-7	breast:
2	chr12:120504107..120508235-chr12:120509191..120512333,4	MCF-7	breast:

Variant related genes	Relation type
CCDC64	TF binding region
ENSG00000135127	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10128766	1.00[ASW][hapmap];0.87[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10400498	1.00[ASW][hapmap];0.87[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10400560	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10849731	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10849732	0.91[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs10849735	0.91[CHB][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs10849736	1.00[ASW][hapmap];0.87[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.94[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11064987	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11064988	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11064996	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11065003	1.00[ASW][hapmap];0.87[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11833221	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12310269	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12310591	0.96[ASN][1000 genomes]
rs12313413	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12318774	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12320793	0.88[ASN][1000 genomes]
rs12322236	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12422923	0.96[ASN][1000 genomes]
rs16949901	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16949946	1.00[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.84[MEX][hapmap];0.80[MKK][hapmap];0.94[TSI][hapmap];0.81[YRI][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16949961	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17841967	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2239200	0.86[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2239201	0.86[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2239202	0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2239203	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2239204	0.94[ASN][1000 genomes]
rs2240311	0.87[CHB][hapmap]
rs2283359	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2283360	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2286040	1.00[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28726166	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3742042	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3852586	0.83[CHB][hapmap]
rs4105713	0.81[ASN][1000 genomes]
rs4767869	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4767871	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4767872	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4767875	0.96[ASN][1000 genomes]
rs4767876	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58272825	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59168361	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60466490	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6490281	0.86[CHB][hapmap];0.86[CHD][hapmap];0.81[ASN][1000 genomes]
rs6490284	0.83[CHB][hapmap]
rs7298183	0.90[ASN][1000 genomes]
rs7298727	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7300023	0.86[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7306739	0.83[CHB][hapmap]
rs7312971	0.91[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs7397339	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7958402	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7958497	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7968557	0.87[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7978927	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3525916	chr12:120345352-120665045	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	esv3525917	chr12:120345352-120665045	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
3	nsv899554	chr12:120389613-120513625	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7965829	CCDC64	cis	cerebellum	SCAN
rs7965829	VPS33A	cis	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120486800-120512000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr12:120487800-120512200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr12:120493800-120523800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr12:120494800-120517800	Weak transcription	Lung	lung
5	chr12:120497600-120507400	Enhancers	Stomach Mucosa	stomach
6	chr12:120497600-120509400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr12:120498200-120507400	Strong transcription	Primary T cells from cord blood	blood
8	chr12:120498400-120511600	Strong transcription	Primary T helper cells PMA-I stimulated	--
9	chr12:120498800-120516600	Weak transcription	Fetal Brain Male	brain
10	chr12:120499200-120507800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr12:120499400-120509400	Weak transcription	Pancreas	Pancrea
12	chr12:120499800-120511200	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr12:120499800-120516400	Weak transcription	Primary B cells from cord blood	blood
14	chr12:120502000-120523400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr12:120502200-120509600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr12:120502200-120509600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr12:120502200-120516600	Weak transcription	Duodenum Mucosa	Duodenum
18	chr12:120502200-120517800	Weak transcription	Gastric	stomach
19	chr12:120502400-120523200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr12:120502400-120523400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr12:120502400-120524400	Weak transcription	Fetal Intestine Small	intestine
22	chr12:120502600-120518400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr12:120502600-120524400	Weak transcription	Brain Anterior Caudate	brain
24	chr12:120502600-120525200	Weak transcription	Spleen	Spleen
25	chr12:120502800-120514200	Weak transcription	Hela-S3	cervix
26	chr12:120503000-120509400	Weak transcription	Primary B cells from peripheral blood	blood
27	chr12:120503000-120509600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr12:120503000-120509600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr12:120503000-120517000	Weak transcription	Dnd41	blood
30	chr12:120503400-120509400	Weak transcription	Fetal Thymus	thymus
31	chr12:120503600-120509400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr12:120503600-120509400	Weak transcription	Brain Cingulate Gyrus	brain
33	chr12:120503600-120509600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr12:120503600-120509600	Weak transcription	Esophagus	oesophagus
35	chr12:120503600-120509600	Weak transcription	Fetal Brain Female	brain
36	chr12:120503600-120516000	Weak transcription	Brain Hippocampus Middle	brain
37	chr12:120503800-120509400	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr12:120503800-120512000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr12:120503800-120518000	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr12:120504200-120510200	Weak transcription	Brain Angular Gyrus	brain
41	chr12:120504600-120509400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr12:120504600-120509400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr12:120504600-120516800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr12:120504600-120516800	Weak transcription	HMEC	breast
45	chr12:120504800-120510200	Weak transcription	NHEK	skin
46	chr12:120505800-120509600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr12:120505800-120516600	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr12:120506000-120508800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr12:120506000-120509000	Weak transcription	Thymus	Thymus
50	chr12:120506600-120507400	Enhancers	HepG2	liver

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