Variant report

Variant	rs6787493
Chromosome Location	chr3:52528000-52528001
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:52526972-52528773	K562	blood:	n/a	n/a
2	MTA3	chr3:52527761-52528079	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:52527697-52528396	GM12878	blood:	n/a	n/a
4	POLR2A	chr3:52527455-52528368	U87	brain:	n/a	n/a
5	POLR2A	chr3:52527049-52528033	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr3:52527202-52528091	HepG2	liver:	n/a	n/a
7	POLR2A	chr3:52527755-52528033	K562	blood:	n/a	n/a
8	POLR2A	chr3:52527642-52528011	HCT-116	colon:	n/a	n/a
9	POLR2A	chr3:52527490-52528414	SK-N-MC	brain:	n/a	n/a
10	POLR2A	chr3:52527145-52528073	GM12892	blood:	n/a	n/a
11	POLR2A	chr3:52527579-52528258	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr3:52527145-52528307	K562	blood:	n/a	n/a
13	POLR2A	chr3:52527473-52528327	U87	brain:	n/a	n/a
14	POLR2A	chr3:52527615-52528059	ECC-1	luminal epithelium:	n/a	n/a
15	POLR2A	chr3:52527443-52528313	Hela-S3	cervix:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52525628..52528041-chr3:52561895..52563443,2	K562	blood:
2	chr3:52525356..52528300-chr3:52566814..52568456,2	MCF-7	breast:
3	chr3:52527250..52529955-chr3:52567199..52569414,2	MCF-7	breast:
4	chr3:52527621..52529302-chr3:52531817..52533690,2	K562	blood:

No data

Variant related genes	Relation type
STAB1	TF binding region
ENSG00000168273	Chromatin interaction
ENSG00000168268	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1011062	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1011064	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1035002	0.91[EUR][1000 genomes]
rs1035003	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10865972	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11721286	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13074649	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1541495	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2109557	0.81[EUR][1000 genomes]
rs2109558	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2109559	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2215466	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2335928	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2335929	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2878549	0.81[EUR][1000 genomes]
rs3755810	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3774409	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs409803	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs419604	0.81[EUR][1000 genomes]
rs4312651	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4687541	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4687543	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4687544	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4687614	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4687616	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4687617	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687618	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4687619	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4687621	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs575476	0.81[EUR][1000 genomes]
rs613519	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6414568	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6445483	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6445484	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6445485	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6445486	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6445506	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs676034	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6771558	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6782162	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6784615	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6810027	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs728408	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs758800	0.93[EUR][1000 genomes]
rs758803	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7620015	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs887514	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs929528	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs929529	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9846089	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9847332	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9850471	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9855470	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9863753	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9867823	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv876793	chr3:52450043-52584787	Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Enhancers 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 target site	37 gene(s)	inside rSNPs	diseases
5	esv1818902	chr3:52481406-52572056	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
7	nsv590304	chr3:52517206-52529266	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:143 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52491600-52528000	Strong transcription	Thymus	Thymus
2	chr3:52491800-52528200	Strong transcription	Cortex derived primary cultured neurospheres	brain
3	chr3:52491800-52528200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr3:52499600-52529200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:52501600-52528800	Strong transcription	Fetal Intestine Small	intestine
6	chr3:52504200-52528000	Strong transcription	Primary B cells from peripheral blood	blood
7	chr3:52504200-52528000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr3:52504200-52528600	Strong transcription	Brain Germinal Matrix	brain
9	chr3:52504400-52528000	Strong transcription	Fetal Brain Female	brain
10	chr3:52504800-52528000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr3:52508000-52532200	Weak transcription	K562	blood
12	chr3:52509400-52528000	Strong transcription	Gastric	stomach
13	chr3:52509600-52528200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr3:52510600-52528600	Weak transcription	Fetal Brain Male	brain
15	chr3:52511400-52528000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr3:52513400-52541400	Weak transcription	A549	lung
17	chr3:52513600-52530000	Weak transcription	Fetal Kidney	kidney
18	chr3:52514600-52534200	Weak transcription	Small Intestine	intestine
19	chr3:52515600-52528400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr3:52517200-52528200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr3:52518800-52528000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:52518800-52528000	Strong transcription	Aorta	Aorta
23	chr3:52519000-52528200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr3:52519000-52528600	Weak transcription	Fetal Heart	heart
25	chr3:52519400-52528000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr3:52519400-52530000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr3:52520400-52528000	Strong transcription	Ovary	ovary
28	chr3:52521000-52529800	Weak transcription	Hela-S3	cervix
29	chr3:52521800-52528200	Genic enhancers	Spleen	Spleen
30	chr3:52522600-52529400	Weak transcription	Psoas Muscle	Psoas
31	chr3:52522800-52528200	Genic enhancers	Right Ventricle	heart
32	chr3:52523600-52528400	Genic enhancers	Lung	lung
33	chr3:52523600-52528800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr3:52523800-52528200	Genic enhancers	Fetal Muscle Trunk	muscle
35	chr3:52524000-52528200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr3:52524200-52528000	Strong transcription	Fetal Stomach	stomach
37	chr3:52524400-52529400	Weak transcription	NHDF-Ad	bronchial
38	chr3:52524600-52528200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr3:52524800-52528400	Strong transcription	NHLF	lung
40	chr3:52525000-52528400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
41	chr3:52525400-52528000	Strong transcription	Esophagus	oesophagus
42	chr3:52525600-52528400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr3:52526000-52530200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr3:52526200-52529000	Enhancers	HUVEC	blood vessel
45	chr3:52526600-52528000	Strong transcription	Brain Hippocampus Middle	brain
46	chr3:52526800-52528400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr3:52526800-52528600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr3:52526800-52529400	Weak transcription	HepG2	liver
49	chr3:52527000-52528000	Weak transcription	Primary hematopoietic stem cells	blood
50	chr3:52527000-52528000	Weak transcription	Duodenum Smooth Muscle	Duodenum

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