Variant report

Variant	rs11712075
Chromosome Location	chr3:43363205-43363206
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:43359634..43362364-chr3:43362365..43365194,3	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11130000	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11708097	0.86[ASW][hapmap];0.87[CEU][hapmap];0.97[GIH][hapmap];0.85[TSI][hapmap]
rs11708173	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11709517	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs11710079	0.87[CEU][hapmap]
rs11710107	0.87[CEU][hapmap];0.97[GIH][hapmap];0.82[TSI][hapmap]
rs11710253	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11710955	0.87[CEU][hapmap];0.97[GIH][hapmap];0.85[TSI][hapmap]
rs11711651	0.84[EUR][1000 genomes]
rs11711758	0.86[ASW][hapmap];0.87[CEU][hapmap];0.97[GIH][hapmap];0.85[TSI][hapmap]
rs11715609	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11717380	0.86[CEU][hapmap]
rs11719258	0.87[EUR][1000 genomes]
rs13079636	0.87[CEU][hapmap]
rs13082581	0.87[EUR][1000 genomes]
rs13084604	0.97[GIH][hapmap]
rs13098202	0.97[GIH][hapmap]
rs1384434	0.86[CEU][hapmap];0.97[GIH][hapmap];0.82[TSI][hapmap]
rs1482648	0.97[GIH][hapmap]
rs1482650	0.87[CEU][hapmap];0.97[GIH][hapmap];0.85[TSI][hapmap]
rs1506615	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1506616	0.86[ASW][hapmap];0.87[CEU][hapmap];0.97[GIH][hapmap];0.85[TSI][hapmap]
rs17407870	0.97[GIH][hapmap]
rs17407912	0.97[GIH][hapmap]
rs17643558	0.87[GIH][hapmap]
rs2086653	0.97[GIH][hapmap]
rs2219902	0.97[GIH][hapmap]
rs2372433	0.97[GIH][hapmap]
rs2888312	0.82[CEU][hapmap];0.97[GIH][hapmap];0.85[TSI][hapmap]
rs34031620	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs35690908	0.87[EUR][1000 genomes]
rs4564953	0.87[CEU][hapmap]
rs66498110	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6768557	0.97[GIH][hapmap]
rs6782442	0.97[GIH][hapmap]
rs73072960	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs73075063	0.87[EUR][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	nsv1009102	chr3:43285369-43369712	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11712075	CXCR6	cis	cerebellum	SCAN
rs11712075	TMEM42	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43332800-43377000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:43340600-43365600	Weak transcription	Esophagus	oesophagus
3	chr3:43345000-43368200	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr3:43345400-43367400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr3:43345600-43364400	Weak transcription	HMEC	breast
6	chr3:43346000-43377000	Weak transcription	K562	blood
7	chr3:43346400-43367200	Weak transcription	Fetal Lung	lung
8	chr3:43348400-43378800	Weak transcription	Hela-S3	cervix
9	chr3:43350000-43367400	Weak transcription	Aorta	Aorta
10	chr3:43350400-43365800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:43351000-43375600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr3:43353000-43374000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr3:43353200-43367400	Weak transcription	Dnd41	blood
14	chr3:43353400-43375200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr3:43354400-43369600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr3:43355000-43364600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:43356400-43363600	Enhancers	Adipose Nuclei	Adipose
18	chr3:43356600-43363600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
19	chr3:43357800-43363600	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr3:43359200-43367000	Weak transcription	Colon Smooth Muscle	Colon
21	chr3:43359400-43366400	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr3:43359400-43366800	Weak transcription	Small Intestine	intestine
23	chr3:43359400-43367800	Weak transcription	Stomach Mucosa	stomach
24	chr3:43359400-43374000	Weak transcription	Placenta	Placenta
25	chr3:43359400-43376600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr3:43359600-43363400	Enhancers	Liver	Liver
27	chr3:43359600-43364600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr3:43359600-43366200	Weak transcription	Brain Substantia Nigra	brain
29	chr3:43359600-43367000	Weak transcription	Fetal Intestine Large	intestine
30	chr3:43359600-43367200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr3:43359600-43367200	Weak transcription	Duodenum Mucosa	Duodenum
32	chr3:43359600-43367200	Weak transcription	Fetal Heart	heart
33	chr3:43359600-43367400	Weak transcription	Fetal Stomach	stomach
34	chr3:43359600-43367400	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr3:43359600-43367800	Weak transcription	Brain Anterior Caudate	brain
36	chr3:43359600-43371800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr3:43359600-43372000	Weak transcription	NHLF	lung
38	chr3:43359600-43372200	Weak transcription	HSMM	muscle
39	chr3:43359600-43375400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr3:43359600-43376200	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr3:43359800-43364800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr3:43359800-43365000	Weak transcription	Primary B cells from peripheral blood	blood
43	chr3:43359800-43367200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr3:43359800-43367600	Weak transcription	HSMMtube	muscle
45	chr3:43359800-43368000	Weak transcription	Fetal Kidney	kidney
46	chr3:43359800-43368400	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr3:43359800-43369800	Weak transcription	NHEK	skin
48	chr3:43360200-43365000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:43360200-43368600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr3:43360400-43364800	Strong transcription	HUVEC	blood vessel

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