Variant report

Variant	rs10085696
Chromosome Location	chr7:69783020-69783021
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1014059	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10262697	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10499813	0.84[ASN][1000 genomes]
rs12113555	0.84[ASN][1000 genomes]
rs12155144	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12698841	0.80[ASN][1000 genomes]
rs12698843	0.81[ASN][1000 genomes]
rs12698846	0.81[ASN][1000 genomes]
rs12698847	0.81[ASN][1000 genomes]
rs12698853	0.83[ASN][1000 genomes]
rs12698856	0.84[ASN][1000 genomes]
rs12698857	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12698859	0.81[ASN][1000 genomes]
rs12698862	0.82[ASN][1000 genomes]
rs12698869	0.84[ASN][1000 genomes]
rs12698875	0.86[ASN][1000 genomes]
rs12698879	0.90[ASN][1000 genomes]
rs12698880	0.90[ASN][1000 genomes]
rs12698882	0.85[EUR][1000 genomes]
rs12698883	0.85[EUR][1000 genomes]
rs12698884	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12698886	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12698892	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12698893	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12698895	0.81[JPT][hapmap]
rs13229686	0.85[EUR][1000 genomes]
rs13238017	0.85[EUR][1000 genomes]
rs13242485	0.80[ASN][1000 genomes]
rs13247796	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs13340492	0.90[EUR][1000 genomes]
rs1404275	0.90[ASN][1000 genomes]
rs1476104	0.81[ASN][1000 genomes]
rs17365333	0.81[ASN][1000 genomes]
rs17604001	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17762460	0.85[EUR][1000 genomes]
rs1880369	0.84[ASN][1000 genomes]
rs2030705	0.81[EUR][1000 genomes]
rs2030706	0.85[EUR][1000 genomes]
rs2866275	0.85[EUR][1000 genomes]
rs35062112	0.90[ASN][1000 genomes]
rs4475377	0.90[ASN][1000 genomes]
rs66936223	0.90[EUR][1000 genomes]
rs6943610	0.81[ASN][1000 genomes]
rs6943630	0.82[ASN][1000 genomes]
rs6945241	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6946066	0.84[ASN][1000 genomes]
rs6948676	0.84[ASN][1000 genomes]
rs6953075	0.90[EUR][1000 genomes]
rs6964139	0.82[ASN][1000 genomes]
rs6971237	0.85[EUR][1000 genomes]
rs6975814	0.90[EUR][1000 genomes]
rs6978841	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6978919	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs735060	0.81[ASN][1000 genomes]
rs7779308	0.80[ASN][1000 genomes]
rs7782771	0.84[ASN][1000 genomes]
rs7783592	0.84[ASN][1000 genomes]
rs7790084	0.81[ASN][1000 genomes]
rs7791954	0.84[ASN][1000 genomes]
rs7803814	0.84[ASN][1000 genomes]
rs7807263	0.84[ASN][1000 genomes]
rs7808588	0.90[ASN][1000 genomes]
rs870919	0.84[ASN][1000 genomes]
rs9638582	0.81[ASN][1000 genomes]
rs9647931	0.88[EUR][1000 genomes]
rs9647932	0.90[EUR][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	nsv1018749	chr7:69149029-69995112	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv532782	chr7:69383651-70189959	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv916345	chr7:69520612-69784809	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv869342	chr7:69671501-69958576	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv607431	chr7:69699074-69828729	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv888337	chr7:69707076-69952187	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv529669	chr7:69709373-69974708	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1028870	chr7:69742438-69879231	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10085696	RABGEF1	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:69776000-69786600	Enhancers	Primary T cells from cord blood	blood
2	chr7:69778600-69789600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr7:69779000-69783400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr7:69779000-69783600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr7:69779000-69784000	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr7:69779200-69783600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr7:69779200-69783800	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr7:69779200-69784400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr7:69779400-69783400	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr7:69779400-69783800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr7:69779400-69783800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr7:69779600-69802200	Weak transcription	Primary B cells from cord blood	blood
13	chr7:69780800-69785800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr7:69781200-69784400	Enhancers	Primary T cells fromperipheralblood	blood
15	chr7:69781600-69783800	Enhancers	Lung	lung
16	chr7:69781600-69784000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr7:69781600-69784800	Enhancers	Dnd41	blood
18	chr7:69781800-69783400	Enhancers	Pancreas	Pancrea
19	chr7:69781800-69783600	Enhancers	Rectal Smooth Muscle	rectum
20	chr7:69781800-69783800	Enhancers	Esophagus	oesophagus
21	chr7:69781800-69784000	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr7:69781800-69784400	Enhancers	Fetal Thymus	thymus
23	chr7:69782000-69783800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr7:69782000-69788000	Weak transcription	Left Ventricle	heart
25	chr7:69782200-69783400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr7:69782600-69783800	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr7:69782600-69783800	Enhancers	Brain Anterior Caudate	brain
28	chr7:69782800-69783200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr7:69782800-69783400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr7:69782800-69783800	Weak transcription	Colon Smooth Muscle	Colon
31	chr7:69782800-69784200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr7:69782800-69784400	Weak transcription	Aorta	Aorta
33	chr7:69782800-69785400	Weak transcription	Brain Hippocampus Middle	brain
34	chr7:69782800-69786200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr7:69782800-69786200	Weak transcription	Gastric	stomach
36	chr7:69782800-69787600	Weak transcription	Fetal Stomach	stomach
37	chr7:69782800-69787800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr7:69782800-69790400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr7:69782800-69790400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr7:69783000-69783800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr7:69783000-69785600	Weak transcription	NHEK	skin
42	chr7:69783000-69785800	Weak transcription	HMEC	breast
43	chr7:69783000-69790400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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