Variant report

Variant	rs17052051
Chromosome Location	chr3:52331266-52331267
allele	C/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	MAFK	chr3:52331233-52331633	HepG2	liver:	n/a	chr3:52331399-52331409
3	POLR2A	chr3:52326828-52335551	HepG2	liver:	n/a	n/a
4	POLR2A	chr3:52330489-52334598	HepG2	liver:	n/a	n/a
5	CTCF	chr3:52331220-52331370	HepG2	liver:	n/a	n/a
6	POLR2A	chr3:52331179-52332232	HepG2	liver:	n/a	n/a
7	POLR2A	chr3:52331151-52332056	K562	blood:	n/a	n/a
8	CTCF	chr3:52331220-52331370	HRPEpiC	eye:	n/a	n/a
9	POLR2A	chr3:52331185-52331793	GM12878	blood:	n/a	n/a
10	POLR2A	chr3:52326795-52334549	HepG2	liver:	n/a	n/a
11	POLR2A	chr3:52331220-52331408	H1-hESC	embryonic stem cell:	n/a	n/a
12	MAFK	chr3:52331232-52331476	IMR90	lung:	n/a	chr3:52331399-52331409
13	MAFK	chr3:52331255-52331546	K562	blood:	n/a	chr3:52331399-52331409
14	POLR2A	chr3:52330801-52332110	HepG2	liver:	n/a	n/a
15	POLR2A	chr3:52326721-52333108	HepG2	liver:	n/a	n/a
16	CTCF	chr3:52331200-52331350	K562	blood:	n/a	n/a
17	MAFF	chr3:52331231-52331546	HepG2	liver:	n/a	chr3:52331397-52331415
18	POLR2A	chr3:52331175-52331467	HepG2	liver:	n/a	n/a
19	HEY1	chr3:52331218-52331742	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	chr3:52329944..52331770-chr3:52331986..52334614,2	MCF-7	breast:
4	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: 81 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10460962	1.00[CEU][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10461027	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs10461028	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10865971	1.00[CEU][hapmap]
rs11706515	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs11706541	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11707056	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs11708581	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs11708811	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs11710014	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11711914	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11711974	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11713914	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs11714313	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11714358	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11715208	0.96[EUR][1000 genomes]
rs11715382	0.87[EUR][1000 genomes]
rs11715391	1.00[CEU][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11716487	1.00[CEU][hapmap]
rs11717028	0.93[EUR][1000 genomes]
rs11717574	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11718125	0.83[AFR][1000 genomes]
rs11718729	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719760	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720365	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs11721277	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17052052	1.00[CEU][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17052053	1.00[CEU][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17052054	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17263770	1.00[CEU][hapmap]
rs1767	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1769	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35976326	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3733063	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3852062	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3886875	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs4082828	1.00[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55676974	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55806905	0.90[EUR][1000 genomes]
rs55813842	0.90[EUR][1000 genomes]
rs55847657	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56002041	0.90[EUR][1000 genomes]
rs56322342	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56352611	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56899118	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57849650	0.90[EUR][1000 genomes]
rs58531656	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60382084	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61644644	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61729402	1.00[ASN][1000 genomes]
rs61729450	1.00[ASN][1000 genomes]
rs6445385	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6783652	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6793317	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809248	1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs724801	1.00[CEU][hapmap]
rs729555	1.00[CEU][hapmap]
rs73072990	0.84[EUR][1000 genomes]
rs73088773	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73088783	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73088785	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73088791	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73088800	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73091166	0.90[EUR][1000 genomes]
rs73091168	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs746239	0.90[EUR][1000 genomes]
rs7615405	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7628461	1.00[CEU][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7633687	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7638204	1.00[CEU][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7643913	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9844183	0.82[YRI][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17052051	PPM1M	cis	Nerve Tibial	GTEx
rs17052051	PPM1M	cis	Artery Tibial	GTEx

Chromatin state (count:100 , 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	chr3:52322800-52331400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr3:52322800-52331400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:52322800-52331600	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr3:52322800-52331800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:52323000-52332600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr3:52323200-52341000	Weak transcription	Small Intestine	intestine
10	chr3:52323400-52333200	Weak transcription	HUVEC	blood vessel
11	chr3:52324000-52331800	Weak transcription	K562	blood
12	chr3:52324000-52332800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr3:52324200-52331400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr3:52324400-52332000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:52325000-52332000	Strong transcription	Right Ventricle	heart
16	chr3:52325600-52331600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr3:52325600-52340400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr3:52325800-52332000	Weak transcription	Fetal Kidney	kidney
19	chr3:52326600-52332200	Genic enhancers	Fetal Intestine Small	intestine
20	chr3:52326800-52331600	Weak transcription	NHEK	skin
21	chr3:52327000-52331800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:52327200-52331800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:52327200-52332000	Weak transcription	Ovary	ovary
24	chr3:52327200-52332600	Weak transcription	Left Ventricle	heart
25	chr3:52327200-52333200	Weak transcription	GM12878-XiMat	blood
26	chr3:52327200-52333800	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr3:52327200-52351600	Weak transcription	Aorta	Aorta
28	chr3:52327400-52331800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr3:52327400-52331800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:52327400-52331800	Weak transcription	Osteobl	bone
31	chr3:52327400-52338400	Weak transcription	Rectal Smooth Muscle	rectum
32	chr3:52327400-52351600	Weak transcription	Brain Anterior Caudate	brain
33	chr3:52327600-52331400	Weak transcription	Pancreas	Pancrea
34	chr3:52327600-52334000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:52327600-52344600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr3:52327800-52331800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:52327800-52333200	Weak transcription	Colonic Mucosa	Colon
38	chr3:52327800-52333800	Weak transcription	Esophagus	oesophagus
39	chr3:52328000-52331400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:52328000-52331400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:52328000-52331600	Weak transcription	HepG2	liver
42	chr3:52328000-52331600	Weak transcription	HSMMtube	muscle
43	chr3:52328000-52333000	Enhancers	Liver	Liver
44	chr3:52328000-52334200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:52328000-52337000	Weak transcription	Adipose Nuclei	Adipose
46	chr3:52328000-52347000	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr3:52328200-52331400	Weak transcription	Fetal Lung	lung
48	chr3:52328200-52332800	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr3:52328200-52333200	Weak transcription	Gastric	stomach
50	chr3:52328200-52334200	Weak transcription	Rectal Mucosa Donor 31	rectum

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