Variant report

Variant	rs11708173
Chromosome Location	chr3:43405227-43405228
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:43403132..43406596-chr3:43407199..43410614,3	K562	blood:
2	chr3:43404577..43407359-chr3:43418115..43420347,2	K562	blood:

Variant related genes	Relation type
ENSG00000160746	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11130000	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11706123	0.87[EUR][1000 genomes]
rs11708097	0.86[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs11709165	0.87[EUR][1000 genomes]
rs11709517	1.00[ASW][hapmap];0.87[CEU][hapmap];0.85[GIH][hapmap];0.97[TSI][hapmap]
rs11710079	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs11710107	0.91[CEU][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs11710253	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11710486	0.83[EUR][1000 genomes]
rs11710955	0.91[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs11711651	0.99[EUR][1000 genomes]
rs11711758	0.86[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs11712075	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11712894	0.87[EUR][1000 genomes]
rs11713382	0.84[EUR][1000 genomes]
rs11714015	1.00[GIH][hapmap]
rs11715609	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11715896	0.86[CHD][hapmap]
rs11717380	0.90[CEU][hapmap]
rs11717449	0.85[EUR][1000 genomes]
rs11719258	0.96[EUR][1000 genomes]
rs13061553	0.87[EUR][1000 genomes]
rs13079636	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs13082581	0.93[EUR][1000 genomes]
rs13084604	1.00[GIH][hapmap]
rs13092838	1.00[GIH][hapmap]
rs13097209	0.80[EUR][1000 genomes]
rs13098202	1.00[GIH][hapmap]
rs1384434	0.91[CEU][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs1482648	1.00[GIH][hapmap]
rs1482650	0.91[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs1506615	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1506616	0.86[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs17407870	1.00[GIH][hapmap]
rs17407912	1.00[GIH][hapmap]
rs17643558	0.90[GIH][hapmap];0.85[LWK][hapmap]
rs2086653	1.00[GIH][hapmap]
rs2219902	1.00[GIH][hapmap]
rs2372433	1.00[GIH][hapmap]
rs2888312	0.87[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs34031620	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34548104	0.85[EUR][1000 genomes]
rs34898315	0.85[EUR][1000 genomes]
rs35015014	0.85[EUR][1000 genomes]
rs35323779	0.87[EUR][1000 genomes]
rs35690908	0.95[EUR][1000 genomes]
rs4564953	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs4682892	1.00[GIH][hapmap]
rs6441775	0.85[EUR][1000 genomes]
rs66498110	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67032102	0.85[EUR][1000 genomes]
rs6767983	0.84[EUR][1000 genomes]
rs6768557	1.00[GIH][hapmap]
rs6781290	0.87[EUR][1000 genomes]
rs6782442	1.00[GIH][hapmap]
rs6809134	1.00[GIH][hapmap]
rs73072960	0.95[AFR][1000 genomes]
rs73075063	0.96[EUR][1000 genomes]
rs7428158	0.97[GIH][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11708173	CXCR6	cis	cerebellum	SCAN
rs11708173	TMEM42	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43390600-43406600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:43390600-43407200	Weak transcription	Gastric	stomach
3	chr3:43391400-43405400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:43391600-43436000	Weak transcription	Colonic Mucosa	Colon
5	chr3:43392200-43419600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr3:43395800-43406600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:43396000-43405600	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr3:43396800-43407000	Weak transcription	Aorta	Aorta
9	chr3:43396800-43407200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:43397000-43406400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr3:43400000-43419400	Weak transcription	Primary T cells from cord blood	blood
12	chr3:43401400-43414600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:43402000-43407000	Enhancers	Fetal Muscle Leg	muscle
14	chr3:43402200-43405600	Enhancers	HSMMtube	muscle
15	chr3:43402400-43413400	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr3:43402600-43406400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:43402600-43407000	Enhancers	Fetal Muscle Trunk	muscle
18	chr3:43402600-43408600	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr3:43402600-43413600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:43402800-43405400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:43402800-43406800	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr3:43402800-43407200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr3:43403000-43412800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr3:43403000-43419400	Weak transcription	Colon Smooth Muscle	Colon
25	chr3:43403200-43407200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr3:43403400-43406200	Weak transcription	Fetal Brain Female	brain
27	chr3:43403600-43408600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:43403800-43405600	Weak transcription	Brain Germinal Matrix	brain
29	chr3:43403800-43406000	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr3:43403800-43414600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr3:43404000-43405400	Enhancers	Lung	lung
32	chr3:43404000-43405400	Enhancers	Spleen	Spleen
33	chr3:43404000-43406000	Enhancers	Placenta	Placenta
34	chr3:43404000-43406400	Enhancers	Ovary	ovary
35	chr3:43404000-43409400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr3:43404200-43405400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr3:43404200-43405600	Enhancers	Right Ventricle	heart
38	chr3:43404200-43409200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr3:43404200-43411600	Weak transcription	Brain Substantia Nigra	brain
40	chr3:43404200-43413400	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr3:43404400-43406200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr3:43404400-43406200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr3:43404400-43406400	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr3:43404400-43406600	Enhancers	Adipose Nuclei	Adipose
45	chr3:43404600-43405400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr3:43404600-43405600	Enhancers	Stomach Smooth Muscle	stomach
47	chr3:43404600-43405800	Enhancers	Fetal Lung	lung
48	chr3:43404600-43406400	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr3:43404600-43406400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr3:43404600-43406400	Weak transcription	Fetal Intestine Large	intestine

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