Variant report

Variant	rs12701661
Chromosome Location	chr7:38765476-38765477
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 113 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10085487	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap]
rs1012976	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10224856	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10225415	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10225550	1.00[CHB][hapmap]
rs10229055	1.00[CHB][hapmap]
rs10254354	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10270427	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10275873	1.00[CHB][hapmap]
rs10951574	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10951575	1.00[JPT][hapmap]
rs12701653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs12701656	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12701657	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12701671	0.82[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs13224619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13224857	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13229445	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13230196	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs13231372	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs13235997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13238093	0.93[EUR][1000 genomes]
rs1558111	1.00[CHB][hapmap]
rs17240051	1.00[ASN][1000 genomes]
rs17680342	1.00[CEU][hapmap]
rs2040878	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2107742	1.00[JPT][hapmap]
rs2189854	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2190667	1.00[CHB][hapmap]
rs2190670	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs2214667	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2214668	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2215032	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2245773	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286089	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286101	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286103	1.00[JPT][hapmap]
rs2392599	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2392608	1.00[CHB][hapmap]
rs2392610	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34349310	0.93[EUR][1000 genomes]
rs34358406	0.93[EUR][1000 genomes]
rs34621392	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34886315	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34997080	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35220172	1.00[ASN][1000 genomes]
rs35400125	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35632362	0.93[EUR][1000 genomes]
rs35667896	0.85[EUR][1000 genomes]
rs35816439	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35843038	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36004953	0.85[EUR][1000 genomes]
rs36114334	0.89[EUR][1000 genomes]
rs37472	1.00[JPT][hapmap]
rs37473	1.00[JPT][hapmap]
rs37476	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap]
rs37477	1.00[JPT][hapmap]
rs37478	1.00[JPT][hapmap]
rs37479	1.00[JPT][hapmap]
rs4720300	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4720302	1.00[JPT][hapmap]
rs4723780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723781	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723784	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723786	1.00[JPT][hapmap]
rs4723787	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723802	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4723804	1.00[ASN][1000 genomes]
rs57865190	0.91[AFR][1000 genomes]
rs60922992	0.83[AFR][1000 genomes]
rs61155937	0.91[AFR][1000 genomes]
rs6462866	1.00[JPT][hapmap]
rs6462871	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs6462873	1.00[CHB][hapmap];0.82[MEX][hapmap]
rs6947695	1.00[CHB][hapmap]
rs6949958	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6951429	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6960945	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6963090	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6967384	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6971632	1.00[CHB][hapmap]
rs6975410	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6976302	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6976579	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6976580	1.00[CHB][hapmap]
rs6979423	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs71548633	0.96[EUR][1000 genomes]
rs73357129	0.83[AFR][1000 genomes]
rs73357142	0.83[AFR][1000 genomes]
rs73369001	0.89[AFR][1000 genomes]
rs73370706	0.83[AFR][1000 genomes]
rs73370712	0.92[AFR][1000 genomes]
rs73370716	0.91[AFR][1000 genomes]
rs73370730	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73370736	0.91[AFR][1000 genomes]
rs73370740	0.91[AFR][1000 genomes]
rs757685	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs758087	1.00[JPT][hapmap]
rs758088	1.00[ASN][1000 genomes]
rs7782140	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7782277	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7787423	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7790054	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs7793250	1.00[CHB][hapmap]
rs7799887	1.00[CHB][hapmap]
rs7802052	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7803488	1.00[CHB][hapmap]
rs9638945	1.00[CHB][hapmap]
rs976350	1.00[JPT][hapmap]
rs976352	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9886108	1.00[CHB][hapmap];1.00[MEX][hapmap]

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	nsv887965	chr7:38706384-38793243	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12701661	RAB3IL1	trans	brain	seeQTL
rs12701661	VPS41	Cis_1M	lymphoblastoid	RTeQTL
rs12701661	VPS41	cis	multi-tissue	Pritchard

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38749000-38803600	Weak transcription	Fetal Brain Male	brain
2	chr7:38755000-38791200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr7:38755800-38771600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:38757000-38784200	Weak transcription	HMEC	breast
5	chr7:38757200-38835400	Weak transcription	Psoas Muscle	Psoas
6	chr7:38758600-38767000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr7:38758600-38767800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr7:38758600-38780600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr7:38758800-38766400	Weak transcription	Brain Germinal Matrix	brain
10	chr7:38758800-38780000	Weak transcription	Brain Substantia Nigra	brain
11	chr7:38759000-38770600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr7:38759200-38810200	Weak transcription	A549	lung
13	chr7:38759400-38810600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr7:38759600-38779600	Weak transcription	Thymus	Thymus
15	chr7:38759600-38784200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr7:38759800-38768000	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr7:38759800-38780600	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr7:38760000-38773000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr7:38760000-38799800	Weak transcription	HUVEC	blood vessel
20	chr7:38760600-38769800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr7:38760600-38770000	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr7:38760600-38800200	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr7:38760800-38769800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr7:38761000-38820400	Weak transcription	Stomach Mucosa	stomach
25	chr7:38761200-38785400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr7:38761600-38766400	Weak transcription	GM12878-XiMat	blood
27	chr7:38762600-38793200	Weak transcription	Hela-S3	cervix
28	chr7:38763000-38767000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr7:38763200-38828000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr7:38763400-38769800	Strong transcription	Adipose Nuclei	Adipose
31	chr7:38763400-38780400	Weak transcription	Fetal Kidney	kidney
32	chr7:38763400-38792600	Weak transcription	Small Intestine	intestine
33	chr7:38763400-38828800	Weak transcription	HepG2	liver
34	chr7:38763600-38767200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr7:38763600-38772000	Strong transcription	Liver	Liver
36	chr7:38763800-38767400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr7:38763800-38791600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr7:38764000-38769000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr7:38764000-38769400	Strong transcription	Brain Anterior Caudate	brain
40	chr7:38764000-38769800	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr7:38764000-38769800	Strong transcription	Fetal Intestine Small	intestine
42	chr7:38764200-38765600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr7:38764200-38765600	Strong transcription	Spleen	Spleen
44	chr7:38764200-38766200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr7:38764200-38767600	Strong transcription	Aorta	Aorta
46	chr7:38764200-38767600	Strong transcription	Left Ventricle	heart
47	chr7:38764200-38768600	Strong transcription	Brain Cingulate Gyrus	brain
48	chr7:38764200-38768800	Strong transcription	Fetal Muscle Trunk	muscle
49	chr7:38764200-38769400	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr7:38764200-38769800	Strong transcription	Fetal Intestine Large	intestine

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