Variant report

Variant	rs17075597
Chromosome Location	chr3:43396221-43396222
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:43395114-43396768	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr3:43395011-43396918	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr3:43395440-43396756	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr3:43395206-43396682	HUVEC	blood vessel:	n/a	n/a
5	FOSL2	chr3:43395800-43396509	HepG2	liver:	n/a	n/a
6	POLR2A	chr3:43395806-43396446	HL-60	blood:	n/a	n/a
7	POLR2A	chr3:43394957-43396955	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:43390162..43392791-chr3:43393918..43397440,3	K562	blood:

Variant related genes	Relation type
SNRK-AS1	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10865932	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12634274	1.00[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap]
rs13065491	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13320571	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1384433	1.00[CHB][hapmap]
rs1395372	1.00[CHB][hapmap]
rs1588027	1.00[CHB][hapmap];0.94[GIH][hapmap]
rs17075317	0.82[JPT][hapmap]
rs17075535	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17075558	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17075596	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17075600	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17075630	0.82[CHB][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap]
rs17075705	1.00[CHB][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs17075743	1.00[CHB][hapmap];0.81[YRI][hapmap]
rs17075792	1.00[CHB][hapmap]
rs17075814	1.00[CHB][hapmap]
rs2372372	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2372437	1.00[CHB][hapmap]
rs2888298	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4128529	1.00[CHB][hapmap];0.93[YRI][hapmap]
rs4462942	1.00[CHB][hapmap]
rs4510359	1.00[CHB][hapmap];0.94[GIH][hapmap]
rs4586783	1.00[CHB][hapmap]
rs4682678	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4682679	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4682682	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682685	1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[YRI][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4682689	1.00[CHB][hapmap]
rs4682882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683366	1.00[JPT][hapmap]
rs6441772	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6441777	1.00[CHB][hapmap]
rs6770540	1.00[CHB][hapmap]
rs6783741	1.00[CHB][hapmap];0.94[GIH][hapmap]
rs6791641	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6799364	1.00[CHB][hapmap]
rs6800983	1.00[CHB][hapmap];0.94[GIH][hapmap]
rs6803929	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7621298	0.82[JPT][hapmap]
rs7623883	0.81[ASN][1000 genomes]
rs7628317	1.00[CHB][hapmap]
rs7649401	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9311339	1.00[CHB][hapmap];0.94[GIH][hapmap]
rs9681394	0.93[CHD][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs977911	1.00[CHB][hapmap];0.94[GIH][hapmap]
rs9834842	0.89[CEU][hapmap]
rs9836386	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9876172	0.88[MEX][hapmap]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17075597	C1orf194	trans	brain	seeQTL
rs17075597	CAPS	trans	brain	seeQTL
rs17075597	FANK1	trans	brain	seeQTL
rs17075597	CAPSL	trans	brain	seeQTL
rs17075597	TEKT1	trans	brain	seeQTL
rs17075597	SLC47A2	trans	brain	seeQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43381000-43396400	Weak transcription	Stomach Mucosa	stomach
2	chr3:43385200-43396800	Weak transcription	Ovary	ovary
3	chr3:43385800-43402000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:43387600-43402600	Weak transcription	Right Atrium	heart
5	chr3:43389200-43400800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:43390600-43403600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:43390600-43406600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:43390600-43407200	Weak transcription	Gastric	stomach
9	chr3:43390800-43402200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr3:43390800-43405200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr3:43391400-43405400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr3:43391600-43402000	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:43391600-43404200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:43391600-43436000	Weak transcription	Colonic Mucosa	Colon
15	chr3:43392200-43396600	Weak transcription	HSMMtube	muscle
16	chr3:43392200-43419600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr3:43392400-43396400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:43392600-43397000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr3:43392800-43402200	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr3:43393000-43402000	Weak transcription	Left Ventricle	heart
21	chr3:43393000-43405000	Weak transcription	Pancreas	Pancrea
22	chr3:43393400-43396600	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
23	chr3:43393400-43402200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr3:43395000-43396400	ZNF genes & repeats	Primary T cells from cord blood	blood
25	chr3:43395000-43396600	ZNF genes & repeats	Adipose Nuclei	Adipose
26	chr3:43395000-43396600	Enhancers	Liver	Liver
27	chr3:43395200-43396600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr3:43395200-43396600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
29	chr3:43395200-43396600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
30	chr3:43395200-43396600	ZNF genes & repeats	Fetal Stomach	stomach
31	chr3:43395200-43396800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr3:43395200-43396800	ZNF genes & repeats	Primary B cells from cord blood	blood
33	chr3:43395200-43396800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
34	chr3:43395200-43396800	ZNF genes & repeats	Aorta	Aorta
35	chr3:43395200-43396800	ZNF genes & repeats	Fetal Thymus	thymus
36	chr3:43395200-43396800	ZNF genes & repeats	Thymus	Thymus
37	chr3:43395600-43396800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr3:43395600-43397200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:43395800-43406600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr3:43396000-43396600	ZNF genes & repeats	Spleen	Spleen
41	chr3:43396000-43405600	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr3:43396200-43396400	ZNF genes & repeats	Esophagus	oesophagus
43	chr3:43396200-43396600	ZNF genes & repeats	Muscle Satellite Cultured Cells	--

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