Variant report

Variant	rs73088785
Chromosome Location	chr3:52313214-52313215
allele	G/T
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	EP300	chr3:52311125-52315006	SK-N-SH	brain:	n/a	chr3:52313881-52313895 chr3:52312475-52312484 chr3:52311546-52311555 chr3:52313068-52313082 chr3:52313069-52313083
2	SIN3AK20	chr3:52311416-52313328	SK-N-SH	brain:	n/a	n/a
3	UBTF	chr3:52311612-52313457	K562	blood:	n/a	n/a
4	CHD1	chr3:52311281-52313242	GM12878	blood:	n/a	n/a
5	CREB1	chr3:52311473-52313243	HepG2	liver:	n/a	n/a
6	PAX5	chr3:52312428-52313215	GM12878	blood:	n/a	n/a
7	MAZ	chr3:52311174-52313274	IMR90	lung:	n/a	chr3:52311696-52311703 chr3:52312935-52312945
8	RUNX3	chr3:52312080-52313333	GM12878	blood:	n/a	n/a
9	MAX	chr3:52311452-52313631	K562	blood:	n/a	chr3:52311696-52311703 chr3:52312935-52312945
10	CTCF	chr3:52312542-52313343	A549	lung:	n/a	chr3:52312902-52312915 chr3:52312900-52312918
11	REST	chr3:52311264-52313380	H1-neurons	neurons:	n/a	chr3:52311862-52311870 chr3:52311860-52311880
12	MAX	chr3:52311383-52313290	ECC-1	luminal epithelium:	n/a	chr3:52311696-52311703 chr3:52312935-52312945
13	MAX	chr3:52311460-52313365	A549	lung:	n/a	chr3:52311696-52311703 chr3:52312935-52312945
14	POU2F2	chr3:52312726-52313495	GM12891	blood:	n/a	n/a
15	POLR2A	chr3:52311368-52313311	PFSK-1	brain:	n/a	n/a
16	ZNF384	chr3:52312574-52313406	K562	blood:	n/a	n/a
17	POLR2A	chr3:52312028-52313341	H1-hESC	embryonic stem cell:	n/a	n/a
18	CHD1	chr3:52310531-52313715	IMR90	lung:	n/a	n/a
19	MXI1	chr3:52310948-52314914	SK-N-SH	brain:	n/a	n/a
20	POLR2A	chr3:52311345-52313232	U87	brain:	n/a	n/a
21	MTA3	chr3:52311258-52313234	GM12878	blood:	n/a	n/a
22	POLR2A	chr3:52311473-52313658	GM12892	blood:	n/a	n/a
23	PML	chr3:52311346-52313509	GM12878	blood:	n/a	n/a
24	POLR2A	chr3:52311416-52313502	HUVEC	blood vessel:	n/a	n/a
25	ELF1	chr3:52311504-52313530	GM12878	blood:	n/a	n/a
26	ZNF143	chr3:52312025-52313220	GM12878	blood:	n/a	chr3:52312474-52312484
27	POLR2A	chr3:52311101-52313535	GM12878	blood:	n/a	n/a
28	SP1	chr3:52312316-52313383	GM12878	blood:	n/a	n/a
29	POLR2A	chr3:52311553-52313375	MCF-7	breast:	n/a	n/a
30	POLR2A	chr3:52311621-52313237	Hela-S3	cervix:	n/a	n/a
31	MAX	chr3:52311346-52313584	A549	lung:	n/a	chr3:52311696-52311703 chr3:52312935-52312945
32	MYC	chr3:52311548-52313347	A549	lung:	n/a	chr3:52311696-52311703 chr3:52312935-52312945
33	TAF1	chr3:52311534-52313252	H1-hESC	embryonic stem cell:	n/a	n/a
34	RCOR1	chr3:52312158-52313239	K562	blood:	n/a	n/a
35	ZNF384	chr3:52312811-52313230	GM12878	blood:	n/a	n/a
36	POLR2A	chr3:52311448-52313573	HepG2	liver:	n/a	n/a
37	POLR2A	chr3:52311652-52313375	MCF-7	breast:	n/a	n/a
38	POLR2A	chr3:52313203-52313234	HUVEC	blood vessel:	n/a	n/a
39	TAF1	chr3:52311559-52313254	K562	blood:	n/a	n/a
40	POLR2A	chr3:52311387-52313566	K562	blood:	n/a	n/a
41	POLR2A	chr3:52311111-52313571	H1-hESC	embryonic stem cell:	n/a	n/a
42	SMARCB1	chr3:52311645-52313482	Hela-S3	cervix:	n/a	chr3:52312986-52312995
43	POLR2A	chr3:52311366-52313646	GM12892	blood:	n/a	n/a
44	POLR2A	chr3:52311999-52313539	K562	blood:	n/a	n/a
45	POLR2A	chr3:52311136-52313596	GM12878	blood:	n/a	n/a
46	YY1	chr3:52313188-52313563	K562	blood:	n/a	n/a
47	JUN	chr3:52312267-52313299	K562	blood:	n/a	chr3:52312986-52312996 chr3:52312985-52312996 chr3:52312987-52312995 chr3:52312986-52312996
48	TCF12	chr3:52312074-52313223	ECC-1	luminal epithelium:	n/a	n/a
49	RUNX3	chr3:52312062-52313281	GM12878	blood:	n/a	n/a
50	EGR1	chr3:52312315-52313337	HCT-116	colon:	n/a	chr3:52312930-52312943 chr3:52312931-52312945 chr3:52312931-52312942 chr3:52312931-52312942 chr3:52312932-52312942 chr3:52312926-52312948 chr3:52312932-52312942 chr3:52312855-52312865 chr3:52312930-52312944

No.	Distal block	Cell Line	Cell type
1	chr1:28973386..28976212-chr3:52311138..52314136,3	K562	blood:
2	chr3:52269533..52276077-chr3:52310385..52313504,11	MCF-7	breast:
3	chr1:28834867..28836963-chr3:52311963..52313620,2	K562	blood:
4	chr3:52311359..52313564-chr3:52443173..52445594,2	MCF-7	breast:
5	chr3:52312898..52314508-chr3:52316023..52317538,2	MCF-7	breast:
6	chr3:52311763..52314254-chr3:52566006..52568592,3	K562	blood:
7	chr3:52278055..52281861-chr3:52310588..52314481,6	K562	blood:
8	chr3:52312964..52314575-chr3:52349556..52352232,2	K562	blood:
9	chr3:52312779..52315046-chr3:52326364..52328417,2	MCF-7	breast:
10	chr3:52015955..52017820-chr3:52311212..52313632,2	K562	blood:
11	chr3:52297780..52305259-chr3:52310132..52314407,14	MCF-7	breast:
12	chr3:52263321..52268061-chr3:52310039..52314728,5	K562	blood:
13	chr3:52269470..52276026-chr3:52310334..52314212,10	MCF-7	breast:
14	chr3:52310660..52314319-chr3:52321399..52324807,9	K562	blood:
15	chr3:52312419..52314160-chr3:52485786..52488594,2	MCF-7	breast:
16	chr3:52311051..52315983-chr3:52317623..52323290,10	MCF-7	breast:
17	chr3:52263787..52265921-chr3:52311180..52314270,4	MCF-7	breast:
18	chr10:65280826..65281634-chr3:52312597..52313261,2	HCT-116	colon:
19	chr3:52278055..52281861-chr3:52310505..52315451,9	K562	blood:
20	chr3:52028558..52030135-chr3:52311155..52313420,2	K562	blood:
21	chr3:52270811..52274971-chr3:52310538..52315239,11	K562	blood:
22	chr14:23769376..23771868-chr3:52311164..52313739,2	MCF-7	breast:
23	chr3:52187270..52191492-chr3:52311211..52313437,5	MCF-7	breast:
24	chr3:52312722..52314589-chr3:52419579..52422419,2	MCF-7	breast:
25	chr3:52270811..52276588-chr3:52310648..52314131,11	K562	blood:
26	chr3:52278312..52281288-chr3:52312020..52314246,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GLYCTK-1	chr3:52312868-52315151	NONHSAT089909

Variant related genes	Relation type
WDR82	TF binding region
ENSG00000243224	Chromatin interaction
ENSG00000168273	Chromatin interaction
ENSG00000239732	Chromatin interaction
ENSG00000010318	Chromatin interaction
ENSG00000164091	Chromatin interaction
ENSG00000173366	Chromatin interaction
ENSG00000199150	Chromatin interaction
ENSG00000165476	Chromatin interaction
ENSG00000243989	Chromatin interaction
ENSG00000168237	Chromatin interaction
ENSG00000114779	Chromatin interaction
ENSG00000162244	Chromatin interaction
ENSG00000180198	Chromatin interaction
ENSG00000207926	Chromatin interaction
ENSG00000163930	Chromatin interaction
ENSG00000114854	Chromatin interaction
ENSG00000168268	Chromatin interaction
ENSG00000270103	Chromatin interaction
ENSG00000164088	Chromatin interaction
ENSG00000235194	Chromatin interaction
ENSG00000114841	Chromatin interaction
ENSG00000247596	Chromatin interaction
ENSG00000200087	Chromatin interaction
ENSG00000164087	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10460962	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10461027	0.93[EUR][1000 genomes]
rs10461028	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11706515	0.90[EUR][1000 genomes]
rs11706541	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11707056	0.96[EUR][1000 genomes]
rs11708581	0.90[EUR][1000 genomes]
rs11708811	0.96[EUR][1000 genomes]
rs11710014	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11711914	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11711974	0.90[EUR][1000 genomes]
rs11713914	0.90[EUR][1000 genomes]
rs11714313	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11714358	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11715208	0.96[EUR][1000 genomes]
rs11715382	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11715391	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11717028	0.93[EUR][1000 genomes]
rs11717574	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11718125	0.83[AFR][1000 genomes]
rs11718729	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719760	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720365	0.90[EUR][1000 genomes]
rs11721277	0.90[EUR][1000 genomes]
rs17052051	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17052052	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17052053	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17052054	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1767	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1769	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35976326	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3733063	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3852062	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3886875	0.84[EUR][1000 genomes]
rs4082828	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55676974	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55806905	0.90[EUR][1000 genomes]
rs55813842	0.90[EUR][1000 genomes]
rs55847657	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56002041	0.90[EUR][1000 genomes]
rs56322342	0.90[EUR][1000 genomes]
rs56352611	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56899118	0.90[EUR][1000 genomes]
rs57849650	0.90[EUR][1000 genomes]
rs58531656	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60382084	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61644644	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61729402	1.00[ASN][1000 genomes]
rs61729450	1.00[ASN][1000 genomes]
rs6445385	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6783652	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6793317	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809248	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73072990	0.84[EUR][1000 genomes]
rs73088773	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73088783	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73088791	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73088800	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73091166	0.90[EUR][1000 genomes]
rs73091168	0.90[EUR][1000 genomes]
rs746239	0.90[EUR][1000 genomes]
rs7615405	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7628461	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7633687	0.90[EUR][1000 genomes]
rs7638204	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7643913	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs73088785	PPM1M	cis	Nerve Tibial	GTEx
rs73088785	PPM1M	cis	Artery Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52309200-52313600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:52309400-52313400	Active TSS	Right Ventricle	heart
3	chr3:52309600-52313400	Active TSS	Primary T killer memory cells from peripheral blood	blood
4	chr3:52309800-52313400	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr3:52310000-52313400	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr3:52310000-52313400	Active TSS	Ovary	ovary
7	chr3:52310000-52313600	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr3:52310200-52313400	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr3:52310200-52313400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:52310200-52313400	Active TSS	NHDF-Ad	bronchial
11	chr3:52310200-52313600	Active TSS	H1 Cell Line	embryonic stem cell
12	chr3:52310200-52313600	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr3:52310200-52313600	Active TSS	K562	blood
14	chr3:52310200-52314000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr3:52310400-52313400	Active TSS	H9 Cell Line	embryonic stem cell
16	chr3:52310600-52313400	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr3:52310600-52313400	Active TSS	Colonic Mucosa	Colon
18	chr3:52310800-52313400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr3:52310800-52313400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
20	chr3:52310800-52313400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr3:52310800-52313400	Active TSS	Fetal Kidney	kidney
22	chr3:52310800-52313400	Active TSS	Lung	lung
23	chr3:52310800-52313400	Active TSS	Small Intestine	intestine
24	chr3:52310800-52313400	Active TSS	GM12878-XiMat	blood
25	chr3:52310800-52313400	Active TSS	HSMM	muscle
26	chr3:52310800-52313400	Active TSS	HSMMtube	muscle
27	chr3:52310800-52313600	Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr3:52310800-52313800	Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr3:52310800-52314400	Active TSS	Stomach Smooth Muscle	stomach
30	chr3:52311000-52313400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:52311000-52313400	Active TSS	Primary T helper naive cells from peripheral blood	blood
32	chr3:52311000-52313400	Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr3:52311000-52313400	Active TSS	Sigmoid Colon	Sigmoid Colon
34	chr3:52311000-52313400	Active TSS	A549	lung
35	chr3:52311000-52313600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:52311000-52313600	Active TSS	HUES64 Cell Line	embryonic stem cell
37	chr3:52311000-52313600	Active TSS	Aorta	Aorta
38	chr3:52311000-52314000	Active TSS	NHLF	lung
39	chr3:52311000-52314400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr3:52311200-52313400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:52311200-52313400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr3:52311200-52313400	Active TSS	Esophagus	oesophagus
43	chr3:52311200-52313400	Active TSS	Placenta Amnion	Placenta Amnion
44	chr3:52311400-52313400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr3:52311400-52313400	Active TSS	Brain Anterior Caudate	brain
46	chr3:52311400-52313400	Active TSS	Duodenum Mucosa	Duodenum
47	chr3:52311400-52313400	Active TSS	Osteobl	bone
48	chr3:52311400-52314000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
49	chr3:52311400-52314000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr3:52311600-52313400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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