Variant report

Variant	rs20417
Chromosome Location	chr1:186650321-186650322
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	MAX	chr1:186649045-186650512	A549	lung:	n/a	chr1:186650056-186650064
2	POLR2A	chr1:186649021-186650646	HUVEC	blood vessel:	n/a	n/a
3	STAT3	chr1:186650129-186650329	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr1:186649009-186650813	Hela-S3	cervix:	n/a	n/a
5	FOS	chr1:186650195-186650515	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr1:186647362-186650832	PBDE	blood:	n/a	n/a
7	POLR2A	chr1:186648986-186650813	Hela-S3	cervix:	n/a	n/a
8	RCOR1	chr1:186649049-186650711	Hela-S3	cervix:	n/a	n/a
9	ZKSCAN1	chr1:186649117-186650711	Hela-S3	cervix:	n/a	n/a
10	GATA1	chr1:186649122-186650379	PBDE	blood:	n/a	n/a
11	POLR2A	chr1:186647276-186650764	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr1:186648078-186651650	IMR90	lung:	n/a	n/a
13	RFX5	chr1:186648944-186650556	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr1:186646993-186651195	Hela-S3	cervix:	n/a	n/a
15	TCF12	chr1:186648991-186650805	A549	lung:	n/a	n/a
16	CHD2	chr1:186649176-186650578	Hela-S3	cervix:	n/a	n/a
17	CTCF	chr1:186648686-186651449	A549	lung:	n/a	chr1:186651134-186651142
18	TFAP2A	chr1:186649227-186650695	Hela-S3	cervix:	n/a	chr1:186650483-186650494 chr1:186649820-186649834 chr1:186649822-186649832 chr1:186650483-186650494 chr1:186650006-186650017 chr1:186649822-186649832 chr1:186649820-186649834 chr1:186649822-186649832 chr1:186650483-186650494 chr1:186650483-186650494 chr1:186650482-186650496
19	BRCA1	chr1:186650113-186652019	Hela-S3	cervix:	n/a	chr1:186650261-186650268 chr1:186651446-186651453
20	SMC3	chr1:186649044-186650714	Hela-S3	cervix:	n/a	n/a
21	STAT1	chr1:186649155-186650673	Hela-S3	cervix:	n/a	chr1:186649928-186649940 chr1:186650411-186650419 chr1:186650053-186650060
22	POLR2A	chr1:186649201-186650469	GM19193	blood:	n/a	n/a
23	TAF1	chr1:186650212-186650552	Hela-S3	cervix:	n/a	n/a
24	TBP	chr1:186648845-186652253	Hela-S3	cervix:	n/a	n/a
25	MYC	chr1:186650318-186650610	MCF10A-Er-Src	breast:	n/a	n/a
26	TFAP2C	chr1:186649202-186650699	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr1:186648899-186650975	MCF10A-Er-Src	breast:	n/a	n/a
28	STAT3	chr1:186650140-186650340	MCF10A-Er-Src	breast:	n/a	n/a
29	POLR2A	chr1:186649157-186650465	MCF10A-Er-Src	breast:	n/a	n/a
30	MXI1	chr1:186649054-186650718	Hela-S3	cervix:	n/a	n/a
31	ZNF263	chr1:186649146-186650331	HEK293-T-REx	kidney:	n/a	chr1:186649803-186649812
32	POLR2A	chr1:186647207-186651362	Hela-S3	cervix:	n/a	n/a
33	E2F6	chr1:186649765-186650373	H1-hESC	embryonic stem cell:	n/a	chr1:186650320-186650327 chr1:186650320-186650327 chr1:186650004-186650016 chr1:186650008-186650018 chr1:186650011-186650021 chr1:186650320-186650327 chr1:186650316-186650328
34	E2F4	chr1:186650142-186650487	MCF10A-Er-Src	breast:	n/a	chr1:186650320-186650327 chr1:186650320-186650327 chr1:186650320-186650327 chr1:186650316-186650328
35	MAFK	chr1:186649077-186650545	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr1:186649177-186650588	Hela-S3	cervix:	n/a	n/a
37	MAX	chr1:186649107-186650735	Hela-S3	cervix:	n/a	chr1:186650056-186650064
38	CEBPB	chr1:186649073-186650354	Hela-S3	cervix:	n/a	chr1:186649680-186649689 chr1:186649678-186649691 chr1:186649680-186649689 chr1:186649680-186649689

No.	Distal block	Cell Line	Cell type
1	chr1:186649939..186650766-chr9:12429991..12430491,2	Hela-S3	cervix:
2	chr1:186650209..186651033-chr6:89789993..89790875,2	Hela-S3	cervix:
3	chr1:186649823..186650323-chr11:33182661..33183212,2	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PLA2G4A-10	chr1:186649754-186650578	ENSG00000273129.1

Variant related genes	Relation type
PTGS2	TF binding region
ENSG00000176102	Chromatin interaction
ENSG00000271931	Chromatin interaction
ENSG00000247151	Chromatin interaction
ENSG00000146278	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10798048	0.87[CEU][hapmap]
rs10911876	0.86[CEU][hapmap]
rs10911878	0.87[CEU][hapmap]
rs10911886	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs10911900	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10911901	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10911903	0.93[ASN][1000 genomes]
rs10911904	0.93[CEU][hapmap];1.00[CHB][hapmap]
rs10911905	0.93[CEU][hapmap];1.00[CHB][hapmap]
rs10911907	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10911908	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10911909	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10911910	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10911911	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1119066	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1119230	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1119231	0.94[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11583191	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11584118	0.93[ASN][1000 genomes]
rs12057695	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs12064238	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12076624	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12081510	1.00[CHB][hapmap]
rs12084433	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12089049	0.93[ASN][1000 genomes]
rs12401885	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12402603	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12403185	0.86[ASN][1000 genomes]
rs12404145	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs12405141	0.86[ASN][1000 genomes]
rs12405541	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12405919	0.86[ASN][1000 genomes]
rs12409744	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1474596	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs20432	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2066826	0.87[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2143416	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2143417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2179555	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2383515	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2383516	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2383529	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2891247	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs4422959	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4648250	0.82[CHB][hapmap];0.89[ASN][1000 genomes]
rs4648276	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs4648306	0.93[ASN][1000 genomes]
rs4648308	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60203808	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61532952	0.93[ASN][1000 genomes]
rs66494422	0.93[ASN][1000 genomes]
rs6665419	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6666199	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6685280	0.90[ASN][1000 genomes]
rs6698048	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67804662	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67816471	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs68096880	0.93[ASN][1000 genomes]
rs689465	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72721568	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7512750	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs7533973	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs964571	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9783017	0.93[ASN][1000 genomes]
rs9783052	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004481	chr1:186095854-186750968	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv535223	chr1:186095854-186750968	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv2762854	chr1:186547101-186847574	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv872590	chr1:186557453-187500338	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv470750	chr1:186642429-186700959	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv548403	chr1:186642429-186700959	Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186646400-186651000	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr1:186647000-186652000	Active TSS	Stomach Smooth Muscle	stomach
3	chr1:186647600-186651000	Active TSS	A549	lung
4	chr1:186647800-186651800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:186648000-186651200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:186648000-186651600	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr1:186648000-186651800	Active TSS	Colon Smooth Muscle	Colon
8	chr1:186648000-186651800	Active TSS	NHDF-Ad	bronchial
9	chr1:186648200-186650600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:186648200-186651000	Active TSS	Fetal Stomach	stomach
11	chr1:186648200-186651000	Active TSS	Osteobl	bone
12	chr1:186648200-186651200	Active TSS	NH-A	brain
13	chr1:186648400-186650400	Bivalent/Poised TSS	Primary B cells from cord blood	blood
14	chr1:186648400-186650400	Active TSS	Esophagus	oesophagus
15	chr1:186648400-186650800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:186648400-186650800	Active TSS	Colonic Mucosa	Colon
17	chr1:186648400-186650800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
18	chr1:186648400-186651000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr1:186648400-186652000	Active TSS	Right Atrium	heart
20	chr1:186648600-186650400	Active TSS	HUVEC	blood vessel
21	chr1:186648600-186651000	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr1:186648600-186651200	Active TSS	Hela-S3	cervix
23	chr1:186648600-186651400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:186648600-186651400	Active TSS	NHLF	lung
25	chr1:186648600-186651600	Active TSS	HMEC	breast
26	chr1:186648600-186651800	Active TSS	Rectal Smooth Muscle	rectum
27	chr1:186648600-186652000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:186648600-186652000	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr1:186648600-186652400	Active TSS	NHEK	skin
30	chr1:186648800-186650400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
31	chr1:186648800-186650600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr1:186648800-186650800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr1:186648800-186650800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
34	chr1:186648800-186650800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr1:186648800-186650800	Active TSS	Duodenum Mucosa	Duodenum
36	chr1:186648800-186650800	Bivalent/Poised TSS	Fetal Intestine Small	intestine
37	chr1:186649000-186650400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
38	chr1:186649000-186650400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr1:186649000-186650400	Flanking Active TSS	Primary hematopoietic stem cells	blood
40	chr1:186649000-186650400	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
41	chr1:186649000-186650400	Active TSS	Brain Substantia Nigra	brain
42	chr1:186649000-186650400	Active TSS	Fetal Lung	lung
43	chr1:186649000-186650600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
44	chr1:186649000-186650600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
45	chr1:186649000-186650600	Active TSS	H9 Cell Line	embryonic stem cell
46	chr1:186649000-186650600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr1:186649000-186650600	Flanking Active TSS	Adipose Nuclei	Adipose
48	chr1:186649000-186650600	Active TSS	Brain Anterior Caudate	brain
49	chr1:186649000-186650600	Bivalent/Poised TSS	Fetal Brain Female	brain
50	chr1:186649000-186650600	Active TSS	Ovary	ovary

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