Variant report

Variant	rs17052052
Chromosome Location	chr3:52331793-52331794
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	chr3:52327536-52335341	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:52326828-52335551	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:52330489-52334598	HepG2	liver:	n/a	n/a
4	POLR2A	chr3:52331179-52332232	HepG2	liver:	n/a	n/a
5	POLR2A	chr3:52331151-52332056	K562	blood:	n/a	n/a
6	POLR2A	chr3:52331185-52331793	GM12878	blood:	n/a	n/a
7	POLR2A	chr3:52326795-52334549	HepG2	liver:	n/a	n/a
8	POLR2A	chr3:52330801-52332110	HepG2	liver:	n/a	n/a
9	POLR2A	chr3:52326721-52333108	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:52329641..52331855-chr3:52332621..52335782,3	K562	blood:
2	chr3:52330648..52332485-chr3:52338517..52342537,3	K562	blood:
3	chr3:52331076..52332761-chr3:52353981..52355640,2	K562	blood:

Variant related genes	Relation type
MIR135A1	TF binding region
ENSG00000242797	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10460962	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10461027	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10461028	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10865971	1.00[CEU][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs11706515	1.00[CEU][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs11706541	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11707056	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes]
rs11707864	0.83[LWK][hapmap]
rs11708581	0.91[CEU][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs11708811	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs11710014	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11711914	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11711974	1.00[CEU][hapmap];0.88[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11713464	0.81[AMR][1000 genomes]
rs11713914	1.00[CEU][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs11714358	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11714402	0.86[LWK][hapmap]
rs11715208	0.98[EUR][1000 genomes]
rs11715382	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11715391	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11716487	1.00[CEU][hapmap];0.88[TSI][hapmap]
rs11717028	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11718125	0.86[LWK][hapmap]
rs11718729	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11719760	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11720365	1.00[CEU][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs11721277	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13075370	0.80[LWK][hapmap]
rs17052051	1.00[CEU][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17052053	0.91[CEU][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17052054	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17263770	1.00[CEU][hapmap]
rs1767	0.91[CEU][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1769	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35976326	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3733063	0.94[ASW][hapmap];0.91[CEU][hapmap];0.85[LWK][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3886875	1.00[CEU][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs4082828	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55676974	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55806905	0.93[EUR][1000 genomes]
rs55813842	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55847657	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56002041	0.93[EUR][1000 genomes]
rs56322342	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56352611	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56899118	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57849650	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58531656	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58879205	0.81[AMR][1000 genomes]
rs60382084	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61644644	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6445385	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6783652	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6793317	0.91[CEU][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6809248	0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs724801	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs729555	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs73072990	0.87[EUR][1000 genomes]
rs73088773	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73088783	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73088785	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73088791	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73088800	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73091166	0.93[EUR][1000 genomes]
rs73091168	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs746239	0.93[EUR][1000 genomes]
rs7615405	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7628461	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7633687	1.00[CEU][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs7638204	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7643913	0.86[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
3	nsv834694	chr3:52178983-52335821	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases
4	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases
5	nsv876787	chr3:52236762-52367932	Genic enhancers Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
6	nsv876788	chr3:52247110-52367932	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
7	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
8	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
9	nsv834696	chr3:52317478-52479537	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs17052052	DNAH1	cis	parietal	SCAN
rs17052052	SEMA3G	cis	cerebellum	SCAN
rs17052052	NISCH	cis	parietal	SCAN
rs17052052	PPM1M	cis	Artery Tibial	GTEx
rs17052052	PPM1M	cis	parietal	SCAN
rs17052052	TKT	cis	cerebellum	SCAN
rs17052052	ZNF589	cis	cerebellum	SCAN
rs17052052	DNAH1	cis	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52322600-52331800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:52322600-52332000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:52322600-52334400	Weak transcription	NHDF-Ad	bronchial
4	chr3:52322800-52331800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:52323000-52332600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:52323200-52341000	Weak transcription	Small Intestine	intestine
7	chr3:52323400-52333200	Weak transcription	HUVEC	blood vessel
8	chr3:52324000-52331800	Weak transcription	K562	blood
9	chr3:52324000-52332800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:52324400-52332000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:52325000-52332000	Strong transcription	Right Ventricle	heart
12	chr3:52325600-52340400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr3:52325800-52332000	Weak transcription	Fetal Kidney	kidney
14	chr3:52326600-52332200	Genic enhancers	Fetal Intestine Small	intestine
15	chr3:52327000-52331800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:52327200-52331800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr3:52327200-52332000	Weak transcription	Ovary	ovary
18	chr3:52327200-52332600	Weak transcription	Left Ventricle	heart
19	chr3:52327200-52333200	Weak transcription	GM12878-XiMat	blood
20	chr3:52327200-52333800	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr3:52327200-52351600	Weak transcription	Aorta	Aorta
22	chr3:52327400-52331800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:52327400-52331800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr3:52327400-52331800	Weak transcription	Osteobl	bone
25	chr3:52327400-52338400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr3:52327400-52351600	Weak transcription	Brain Anterior Caudate	brain
27	chr3:52327600-52334000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr3:52327600-52344600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr3:52327800-52331800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:52327800-52333200	Weak transcription	Colonic Mucosa	Colon
31	chr3:52327800-52333800	Weak transcription	Esophagus	oesophagus
32	chr3:52328000-52333000	Enhancers	Liver	Liver
33	chr3:52328000-52334200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr3:52328000-52337000	Weak transcription	Adipose Nuclei	Adipose
35	chr3:52328000-52347000	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr3:52328200-52332800	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr3:52328200-52333200	Weak transcription	Gastric	stomach
38	chr3:52328200-52334200	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr3:52328200-52340200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr3:52328200-52366000	Weak transcription	Brain Angular Gyrus	brain
41	chr3:52328600-52340000	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr3:52328800-52332000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr3:52328800-52340200	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr3:52328800-52367600	Weak transcription	Brain Substantia Nigra	brain
45	chr3:52329000-52334400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:52329200-52351600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr3:52329600-52332800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr3:52330000-52335000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr3:52330200-52332000	Weak transcription	Placenta	Placenta
50	chr3:52330200-52332200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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