Variant report

Variant	rs11708097
Chromosome Location	chr3:43465098-43465099
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 123 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs1021049	0.80[CEU][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.82[ASN][1000 genomes]
rs1026887	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1038202	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11130006	0.80[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11706123	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11706130	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11708173	0.86[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs11709165	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11709517	0.86[ASW][hapmap];0.87[CEU][hapmap];0.91[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs11710079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11710107	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11710253	0.88[AMR][1000 genomes]
rs11710486	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11710955	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711651	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11711758	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];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11712894	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11713382	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11714015	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];0.80[TSI][hapmap];0.94[ASN][1000 genomes]
rs11715609	0.81[EUR][1000 genomes]
rs11716569	0.80[CEU][hapmap];0.91[ASN][1000 genomes]
rs11717380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11717449	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11718482	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11719258	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12152260	0.82[ASN][1000 genomes]
rs12374079	0.91[ASN][1000 genomes]
rs13061553	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13072613	0.94[ASN][1000 genomes]
rs13075520	0.94[ASN][1000 genomes]
rs13079636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13082581	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13084604	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13086999	0.94[ASN][1000 genomes]
rs13092838	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.94[ASN][1000 genomes]
rs13097209	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13098202	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.94[ASN][1000 genomes]
rs1384434	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1471643	1.00[ASN][1000 genomes]
rs1471644	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1482648	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.94[ASN][1000 genomes]
rs1482649	0.94[ASN][1000 genomes]
rs1482650	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1482651	0.91[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1482652	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.80[TSI][hapmap];0.91[ASN][1000 genomes]
rs1482653	0.82[ASN][1000 genomes]
rs1506615	0.82[EUR][1000 genomes]
rs1506616	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17030517	0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17407745	1.00[ASN][1000 genomes]
rs17407870	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.80[TSI][hapmap];0.94[ASN][1000 genomes]
rs17407912	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.94[ASN][1000 genomes]
rs17408925	0.94[ASN][1000 genomes]
rs17643558	0.90[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2010778	0.94[ASN][1000 genomes]
rs2054552	0.80[CEU][hapmap];0.87[ASN][1000 genomes]
rs2054553	0.91[ASN][1000 genomes]
rs2054554	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2086653	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];1.00[ASN][1000 genomes]
rs2127725	0.82[ASN][1000 genomes]
rs2170219	0.82[ASN][1000 genomes]
rs2199892	0.94[ASN][1000 genomes]
rs2219902	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.80[TSI][hapmap];0.94[ASN][1000 genomes]
rs2372433	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.94[ASN][1000 genomes]
rs2372436	0.94[ASN][1000 genomes]
rs2372487	0.94[ASN][1000 genomes]
rs2888312	0.87[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3048943	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34031620	0.81[EUR][1000 genomes]
rs34112359	0.85[EUR][1000 genomes]
rs34279519	0.94[ASN][1000 genomes]
rs34548104	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34898315	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34919938	0.84[ASN][1000 genomes]
rs35015014	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35133889	0.94[ASN][1000 genomes]
rs35323779	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35418463	0.94[ASN][1000 genomes]
rs35690908	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3755602	1.00[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs3772165	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3772167	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3821381	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3902207	0.94[ASN][1000 genomes]
rs4564953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs4682690	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4682691	1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4682892	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.94[ASN][1000 genomes]
rs4682897	0.82[ASN][1000 genomes]
rs4682898	0.82[ASN][1000 genomes]
rs6441775	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6441776	0.94[ASN][1000 genomes]
rs6441779	0.92[ASN][1000 genomes]
rs6441780	0.94[ASN][1000 genomes]
rs6441781	0.91[ASN][1000 genomes]
rs6441785	0.83[CEU][hapmap];0.84[ASN][1000 genomes]
rs6441786	0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6441787	0.82[ASN][1000 genomes]
rs66842319	0.94[ASN][1000 genomes]
rs67032102	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6763321	0.87[ASN][1000 genomes]
rs6767983	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6768557	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.94[ASN][1000 genomes]
rs6775337	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6779864	0.82[ASN][1000 genomes]
rs6781290	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6782442	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6797855	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6806339	0.87[ASN][1000 genomes]
rs6809134	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.94[ASN][1000 genomes]
rs73072960	0.84[AMR][1000 genomes]
rs73075063	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7428158	0.81[CHB][hapmap];0.97[GIH][hapmap];0.80[TSI][hapmap];0.83[ASN][1000 genomes]
rs7616708	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7621271	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7648082	0.82[ASN][1000 genomes]
rs7653738	1.00[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9311341	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9682975	0.89[ASN][1000 genomes]
rs9829081	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9851894	0.85[ASN][1000 genomes]
rs9863479	0.91[ASN][1000 genomes]
rs9878330	0.91[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11708097	CXCR6	cis	cerebellum	SCAN
rs11708097	TMEM42	cis	cerebellum	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43432000-43477800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr3:43436400-43475800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr3:43443000-43495600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:43443400-43465800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:43447000-43465800	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr3:43447800-43481200	Weak transcription	Lung	lung
7	chr3:43449000-43473000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr3:43449000-43474400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:43449200-43465600	Weak transcription	HMEC	breast
10	chr3:43451000-43473000	Weak transcription	Duodenum Mucosa	Duodenum
11	chr3:43453600-43467000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:43455600-43475400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr3:43455600-43484400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:43455800-43465800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:43455800-43473000	Weak transcription	Fetal Stomach	stomach
16	chr3:43455800-43473600	Weak transcription	Brain Anterior Caudate	brain
17	chr3:43455800-43477200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr3:43456600-43467200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr3:43457000-43492800	Weak transcription	K562	blood
20	chr3:43459000-43476000	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr3:43459800-43472800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr3:43459800-43496400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:43460400-43466000	Weak transcription	Fetal Intestine Small	intestine
24	chr3:43460600-43466800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr3:43460600-43473000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr3:43460600-43476000	Weak transcription	Spleen	Spleen
27	chr3:43460800-43466000	Weak transcription	Adipose Nuclei	Adipose
28	chr3:43460800-43466400	Weak transcription	Fetal Muscle Leg	muscle
29	chr3:43460800-43473000	Weak transcription	Aorta	Aorta
30	chr3:43460800-43496400	Weak transcription	HSMM	muscle
31	chr3:43461000-43474800	Weak transcription	Brain Hippocampus Middle	brain
32	chr3:43461000-43475400	Weak transcription	Fetal Lung	lung
33	chr3:43461200-43466000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr3:43461200-43476000	Weak transcription	HUVEC	blood vessel
35	chr3:43463000-43472600	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr3:43463800-43465600	Enhancers	Left Ventricle	heart
37	chr3:43464000-43465200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr3:43464000-43465400	Enhancers	Psoas Muscle	Psoas
39	chr3:43464000-43465600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:43464200-43465200	Enhancers	NHLF	lung
41	chr3:43464200-43465600	Enhancers	Colon Smooth Muscle	Colon
42	chr3:43464200-43465600	Enhancers	Fetal Heart	heart
43	chr3:43464200-43465600	Enhancers	Rectal Smooth Muscle	rectum
44	chr3:43464200-43466000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr3:43464400-43465200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr3:43464600-43465600	Enhancers	NHDF-Ad	bronchial
47	chr3:43464600-43465800	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr3:43464600-43465800	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr3:43464600-43466000	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr3:43464800-43465200	Enhancers	Stomach Mucosa	stomach

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