Variant report

Variant	rs683762
Chromosome Location	chr11:77082050-77082051
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:76902781..76903688-chr11:77081021..77082089,5	MCF-7	breast:
2	chr11:77080789..77082811-chr11:77088019..77090076,2	MCF-7	breast:
3	chr11:76906391..76907428-chr11:77080845..77082151,7	MCF-7	breast:
4	chr11:77081708..77083862-chr11:77084179..77086805,3	MCF-7	breast:

Extended variants
information (count: 110 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs11237123	1.00[JPT][hapmap]
rs11237141	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11237142	0.91[ASN][1000 genomes]
rs11237148	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11237150	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11237151	0.91[ASN][1000 genomes]
rs11237164	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1125619	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11512967	0.83[ASN][1000 genomes]
rs1225478	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12361757	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12363707	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12363842	0.91[ASN][1000 genomes]
rs12363944	1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap]
rs12366261	0.81[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.88[ASN][1000 genomes]
rs1237490	0.88[EUR][1000 genomes]
rs12794253	0.91[ASN][1000 genomes]
rs1377472	0.91[ASN][1000 genomes]
rs1597954	0.84[ASN][1000 genomes]
rs1622364	0.91[ASN][1000 genomes]
rs1670446	0.91[ASN][1000 genomes]
rs1670449	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1670450	0.91[ASN][1000 genomes]
rs1670456	0.91[ASN][1000 genomes]
rs1670458	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1670461	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1670462	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs17824184	0.81[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[ASN][1000 genomes]
rs1793468	0.91[ASN][1000 genomes]
rs1793471	0.88[ASN][1000 genomes]
rs1793472	0.91[ASN][1000 genomes]
rs1793487	0.91[ASN][1000 genomes]
rs1793490	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2154754	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs2156567	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2602476	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2602483	0.91[ASN][1000 genomes]
rs2602487	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2725820	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2725822	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2725825	0.91[ASN][1000 genomes]
rs2725828	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3015982	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3015983	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3015985	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];0.92[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3015986	0.93[EUR][1000 genomes]
rs3015988	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs3015990	0.93[EUR][1000 genomes]
rs3015992	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3019233	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3019234	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3019235	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3019236	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3019249	0.87[EUR][1000 genomes]
rs3019257	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34025917	0.89[EUR][1000 genomes]
rs34880271	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4375461	0.91[ASN][1000 genomes]
rs472691	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs476258	0.88[EUR][1000 genomes]
rs479104	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs493256	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs494289	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs503406	0.96[EUR][1000 genomes]
rs505841	0.88[EUR][1000 genomes]
rs508662	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs51500	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs520938	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs522015	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs523481	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs531638	0.87[EUR][1000 genomes]
rs535008	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs552323	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs557484	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs558470	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];0.92[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs560571	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs561386	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];0.92[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs562845	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs563731	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs572485	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs576220	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs580624	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs592602	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs595654	0.87[EUR][1000 genomes]
rs598801	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs644551	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs649040	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs653792	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs657269	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs66518011	0.88[ASN][1000 genomes]
rs66540426	0.91[ASN][1000 genomes]
rs66728428	0.91[ASN][1000 genomes]
rs674259	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs683455	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs684793	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs686068	1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs689108	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7110378	1.00[YRI][hapmap]
rs7118943	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7934230	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7949721	0.92[EUR][1000 genomes]
rs883224	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs883680	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048360	chr11:76900813-77387933	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv541089	chr11:76900813-77387933	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription 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	24 gene(s)	inside rSNPs	diseases
3	nsv1049603	chr11:76900813-77520411	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv541090	chr11:76900813-77520411	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS 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	29 gene(s)	inside rSNPs	diseases
5	esv3424135	chr11:76961603-77277087	Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1037724	chr11:77061945-77250391	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv541091	chr11:77061945-77250391	Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs683762	KCTD14	cis	parietal	SCAN
rs683762	PAK1	cis	parietal	SCAN
rs683762	RSF1	cis	cerebellum	SCAN
rs683762	KCTD14	cis	cerebellum	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77030600-77086800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr11:77033400-77090400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr11:77034400-77086200	Weak transcription	NHLF	lung
4	chr11:77043400-77082400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:77043400-77083600	Weak transcription	Thymus	Thymus
6	chr11:77043800-77088400	Weak transcription	Colonic Mucosa	Colon
7	chr11:77046200-77092400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr11:77046800-77121600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr11:77047200-77096000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr11:77047400-77089000	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr11:77047400-77090000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr11:77048600-77087800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr11:77052600-77085600	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr11:77055000-77085000	Weak transcription	Primary B cells from peripheral blood	blood
15	chr11:77055200-77083400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr11:77055200-77092200	Weak transcription	Small Intestine	intestine
17	chr11:77055200-77117600	Weak transcription	Pancreas	Pancrea
18	chr11:77057400-77088000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr11:77059800-77085800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr11:77059800-77088800	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr11:77060400-77084000	Weak transcription	Fetal Stomach	stomach
22	chr11:77064200-77102800	Weak transcription	Brain Substantia Nigra	brain
23	chr11:77064600-77083000	Weak transcription	Brain Anterior Caudate	brain
24	chr11:77064600-77085400	Weak transcription	Brain Hippocampus Middle	brain
25	chr11:77064800-77085200	Weak transcription	Osteobl	bone
26	chr11:77066000-77084000	Weak transcription	Colon Smooth Muscle	Colon
27	chr11:77066800-77090000	Weak transcription	Brain Angular Gyrus	brain
28	chr11:77067000-77085600	Weak transcription	A549	lung
29	chr11:77067000-77088000	Weak transcription	Gastric	stomach
30	chr11:77067000-77088200	Weak transcription	Liver	Liver
31	chr11:77067000-77092800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr11:77067000-77093800	Weak transcription	Psoas Muscle	Psoas
33	chr11:77067000-77097000	Weak transcription	Esophagus	oesophagus
34	chr11:77067200-77111800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr11:77067600-77083000	Weak transcription	Fetal Kidney	kidney
36	chr11:77068400-77083400	Weak transcription	Aorta	Aorta
37	chr11:77068600-77085600	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr11:77068600-77085800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr11:77068800-77097000	Weak transcription	Brain Cingulate Gyrus	brain
40	chr11:77069000-77083400	Weak transcription	HMEC	breast
41	chr11:77069000-77090000	Weak transcription	Fetal Lung	lung
42	chr11:77069200-77086000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr11:77069600-77085400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr11:77070000-77083200	Weak transcription	Brain Germinal Matrix	brain
45	chr11:77070000-77083800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr11:77070000-77102000	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr11:77070200-77083000	Weak transcription	Duodenum Mucosa	Duodenum
48	chr11:77070200-77083400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr11:77070200-77083400	Weak transcription	Ovary	ovary
50	chr11:77070200-77083400	Weak transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links