Variant report

Variant	rs633789
Chromosome Location	chr1:93723476-93723477
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 146 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:145)

rs_ID	r²[population]
rs1000606	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10430073	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10782958	0.97[EUR][1000 genomes]
rs1081523	0.86[EUR][1000 genomes]
rs1081524	0.88[EUR][1000 genomes]
rs1081525	0.89[EUR][1000 genomes]
rs1081526	0.89[EUR][1000 genomes]
rs10874765	0.93[CEU][hapmap];0.97[EUR][1000 genomes]
rs10874767	0.93[CEU][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes]
rs10874771	0.97[EUR][1000 genomes]
rs10874774	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10874775	0.92[EUR][1000 genomes]
rs1088319	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164878	0.80[EUR][1000 genomes]
rs11164882	0.80[EUR][1000 genomes]
rs11164888	0.98[EUR][1000 genomes]
rs11164889	0.98[EUR][1000 genomes]
rs11164890	0.98[EUR][1000 genomes]
rs11164891	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11164906	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11164911	1.00[ASW][hapmap];0.93[CEU][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11582703	0.97[EUR][1000 genomes]
rs11584466	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12057476	0.96[TSI][hapmap]
rs12067005	0.92[TSI][hapmap]
rs12070900	0.97[EUR][1000 genomes]
rs12071627	0.97[EUR][1000 genomes]
rs12080715	0.96[EUR][1000 genomes]
rs12085959	0.91[CEU][hapmap];0.97[EUR][1000 genomes]
rs12088338	0.82[EUR][1000 genomes]
rs12090723	0.97[EUR][1000 genomes]
rs12731675	0.97[EUR][1000 genomes]
rs12731809	0.97[EUR][1000 genomes]
rs1323626	0.88[EUR][1000 genomes]
rs1323627	0.87[EUR][1000 genomes]
rs1323628	0.93[CEU][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs1414367	0.93[CEU][hapmap];0.92[TSI][hapmap]
rs1535698	0.93[CEU][hapmap];0.97[EUR][1000 genomes]
rs1535700	0.93[CEU][hapmap];0.93[EUR][1000 genomes]
rs1570528	0.93[CEU][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes]
rs17131699	0.92[TSI][hapmap]
rs2031223	0.92[EUR][1000 genomes]
rs2031224	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2104280	0.96[EUR][1000 genomes]
rs2484485	0.93[CEU][hapmap]
rs2749735	0.80[EUR][1000 genomes]
rs2783492	0.80[EUR][1000 genomes]
rs2783498	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs2783506	0.80[EUR][1000 genomes]
rs2815409	0.93[CEU][hapmap];0.92[TSI][hapmap]
rs2815410	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs2815411	0.93[CEU][hapmap];0.80[EUR][1000 genomes]
rs2815413	0.93[CEU][hapmap];0.90[YRI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2815414	0.84[EUR][1000 genomes]
rs4573531	0.97[EUR][1000 genomes]
rs4847239	0.93[CEU][hapmap];0.90[EUR][1000 genomes]
rs4847407	0.97[EUR][1000 genomes]
rs4847409	1.00[ASW][hapmap];0.93[CEU][hapmap];0.97[LWK][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4847411	0.92[EUR][1000 genomes]
rs485622	0.89[EUR][1000 genomes]
rs488646	0.93[CEU][hapmap];0.96[EUR][1000 genomes]
rs504810	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs505531	0.83[EUR][1000 genomes]
rs506556	0.93[CEU][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes]
rs508942	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs512361	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs519723	1.00[CEU][hapmap];0.85[GIH][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs522999	0.91[CEU][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs523262	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs546	0.93[CEU][hapmap];0.92[TSI][hapmap]
rs556888	0.93[CEU][hapmap];0.81[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs558667	0.96[EUR][1000 genomes]
rs559397	0.97[EUR][1000 genomes]
rs56303209	0.97[EUR][1000 genomes]
rs566743	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs571212	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs573056	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[LWK][hapmap];0.99[MKK][hapmap];0.96[TSI][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs581825	0.93[CEU][hapmap];0.90[YRI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs587754	0.97[EUR][1000 genomes]
rs589241	0.94[AMR][1000 genomes]
rs605759	0.90[EUR][1000 genomes]
rs615416	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs626714	0.93[CEU][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes]
rs628714	0.93[CEU][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs629153	0.93[CEU][hapmap];0.91[EUR][1000 genomes]
rs631966	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs637198	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs641390	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6541351	0.86[CEU][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs6541400	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs658178	0.93[CEU][hapmap];0.95[EUR][1000 genomes]
rs658877	0.93[CEU][hapmap];0.90[YRI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs661566	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs662546	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6657587	0.98[EUR][1000 genomes]
rs6664886	0.91[CEU][hapmap];0.93[EUR][1000 genomes]
rs6667701	0.93[CEU][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes]
rs667680	0.84[EUR][1000 genomes]
rs6687359	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs668944	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6701250	0.93[CEU][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs670650	0.96[EUR][1000 genomes]
rs671559	0.83[EUR][1000 genomes]
rs693872	0.92[CEU][hapmap];0.96[EUR][1000 genomes]
rs698926	0.90[EUR][1000 genomes]
rs7413775	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7519163	1.00[ASW][hapmap];0.93[CEU][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7525189	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7529639	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7532015	1.00[ASN][1000 genomes]
rs7534543	0.80[AMR][1000 genomes]
rs7546661	0.89[EUR][1000 genomes]
rs7551635	0.97[EUR][1000 genomes]
rs7554595	0.83[ASN][1000 genomes]
rs7555292	0.93[CEU][hapmap];0.92[TSI][hapmap];0.97[EUR][1000 genomes]
rs771448	0.87[EUR][1000 genomes]
rs771449	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs771450	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs771451	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs771452	0.89[EUR][1000 genomes]
rs771453	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs771456	0.91[EUR][1000 genomes]
rs771457	0.93[CEU][hapmap];0.90[EUR][1000 genomes]
rs771459	0.93[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs771460	0.90[EUR][1000 genomes]
rs771463	0.94[ASW][hapmap];0.93[CEU][hapmap];0.88[LWK][hapmap];0.94[MKK][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs771464	0.92[EUR][1000 genomes]
rs771466	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs771467	0.89[EUR][1000 genomes]
rs771468	0.89[EUR][1000 genomes]
rs771469	0.93[CEU][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs771471	0.89[EUR][1000 genomes]
rs771472	0.89[EUR][1000 genomes]
rs771474	0.89[EUR][1000 genomes]
rs771475	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs771477	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs771480	0.89[EUR][1000 genomes]
rs797660	0.84[EUR][1000 genomes]
rs797669	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs809515	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs810028	0.89[EUR][1000 genomes]
rs812789	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs9432680	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9432700	0.97[EUR][1000 genomes]
rs9432701	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830625	chr1:93566378-93735246	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs633789	RP4-717I23.3	cis	Esophagus Muscularis	GTEx
rs633789	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx
rs633789	RP4-717I23.3	cis	Stomach	GTEx
rs633789	RP4-717I23.3	cis	Artery Tibial	GTEx
rs633789	TMED5	Cis_1M	lymphoblastoid	RTeQTL
rs633789	RP4-717I23.3	cis	Esophagus Mucosa	GTEx
rs633789	RP4-717I23.3	cis	lung	GTEx
rs633789	RP4-717I23.3	cis	Heart Left Ventricle	GTEx
rs633789	LOC646848	cis	normal skin	skin_eQTL
rs633789	RP4-717I23.3	cis	Muscle Skeletal	GTEx
rs633789	RP4-717I23.3	cis	Thyroid	GTEx
rs633789	RP4-717I23.3	cis	Artery Aorta	GTEx
rs633789	RP4-717I23.3	cis	Whole Blood	GTEx
rs633789	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx
rs633789	RP4-717I23.3	cis	Nerve Tibial	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93647000-93756400	Weak transcription	Gastric	stomach
2	chr1:93647200-93757600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:93666600-93727000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr1:93690400-93729400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:93691200-93732400	Weak transcription	HUVEC	blood vessel
6	chr1:93692200-93787800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:93704200-93729800	Weak transcription	Hela-S3	cervix
8	chr1:93706400-93727000	Weak transcription	K562	blood
9	chr1:93707000-93727400	Weak transcription	Liver	Liver
10	chr1:93709000-93724200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:93709000-93726400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:93709000-93727400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:93709000-93728200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:93709000-93728200	Weak transcription	HMEC	breast
15	chr1:93709200-93727400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr1:93709400-93727600	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr1:93709600-93725000	Weak transcription	HepG2	liver
18	chr1:93709600-93725600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:93709600-93727000	Weak transcription	NHEK	skin
20	chr1:93709800-93727000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:93709800-93727000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:93710000-93727000	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr1:93710200-93724200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:93710200-93727000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr1:93710600-93724400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:93711600-93727000	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr1:93713200-93727000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr1:93716200-93728400	Weak transcription	Pancreas	Pancrea
29	chr1:93716800-93727600	Weak transcription	Fetal Kidney	kidney
30	chr1:93717200-93726200	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr1:93717800-93725600	Strong transcription	Dnd41	blood
32	chr1:93717800-93727800	Weak transcription	Ovary	ovary
33	chr1:93718200-93727000	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr1:93718400-93727000	Weak transcription	Fetal Lung	lung
35	chr1:93718400-93727000	Weak transcription	Rectal Smooth Muscle	rectum
36	chr1:93718600-93727000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr1:93718600-93727800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr1:93718600-93728200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr1:93718800-93724400	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr1:93718800-93727000	Weak transcription	Primary B cells from peripheral blood	blood
41	chr1:93718800-93727400	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr1:93718800-93728000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr1:93718800-93728200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr1:93718800-93728200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr1:93719000-93724000	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr1:93719000-93724400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr1:93719000-93727000	Weak transcription	Stomach Smooth Muscle	stomach
48	chr1:93719000-93727400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr1:93719000-93727600	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr1:93719000-93727600	Weak transcription	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links