Variant report

Variant	rs3756809
Chromosome Location	chr6:24776597-24776598
allele	A/C
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:9)
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	chr6:24774693-24777046	GM12892	blood:	n/a	n/a
2	POLR2A	chr6:24776471-24777072	GM12892	blood:	n/a	n/a
3	MXI1	chr6:24776569-24777116	GM12878	blood:	n/a	n/a
4	RUNX3	chr6:24776588-24777013	GM12878	blood:	n/a	n/a
5	POLR2A	chr6:24776541-24777067	GM12878	blood:	n/a	n/a
6	MXI1	chr6:24774525-24777099	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr6:24774582-24777044	K562	blood:	n/a	n/a
8	WRNIP1	chr6:24776561-24776919	GM12878	blood:	n/a	n/a
9	MAX	chr6:24776510-24776992	K562	blood:	n/a	n/a
10	POLR2A	chr6:24776521-24777130	GM12878	blood:	n/a	n/a
11	POLR2A	chr6:24776565-24777098	HepG2	liver:	n/a	n/a
12	MAX	chr6:24776562-24776932	HepG2	liver:	n/a	n/a
13	POLR2A	chr6:24774685-24777071	GM12892	blood:	n/a	n/a
14	POLR2A	chr6:24776342-24776642	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr6:24774738-24777129	HepG2	liver:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:24706431..24709046-chr6:24773872..24777096,3	K562	blood:
2	chr6:24718549..24722818-chr6:24771512..24777723,8	MCF-7	breast:
3	chr6:24666490..24670247-chr6:24774150..24780460,9	K562	blood:
4	chr6:24711892..24724164-chr6:24769415..24786834,81	K562	blood:
5	chr6:24493803..24496211-chr6:24773975..24776646,3	K562	blood:
6	chr6:24522066..24523918-chr6:24775174..24778168,2	K562	blood:
7	chr6:24715365..24725462-chr6:24770390..24783002,86	K562	blood:
8	chr6:24717870..24723661-chr6:24773711..24778808,16	MCF-7	breast:
9	chr6:24665480..24670247-chr6:24773496..24779775,9	K562	blood:

No data

Variant related genes	Relation type
GMNN	TF binding region
ENSG00000111802	Chromatin interaction
ENSG00000112293	Chromatin interaction
ENSG00000112304	Chromatin interaction
ENSG00000112294	Chromatin interaction
ENSG00000272402	Chromatin interaction
ENSG00000112308	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1002649	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs10946726	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11968288	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12183400	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16889670	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16889688	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2295735	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2307306	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2307307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28561768	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3756810	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756811	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756812	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813682	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56208026	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58334728	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58898420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59427770	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59587218	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59904886	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60794509	0.95[ASN][1000 genomes]
rs6456634	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456635	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6901466	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6912564	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6916816	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6917565	1.00[ASN][1000 genomes]
rs6917813	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6934938	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6935339	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6939757	1.00[ASN][1000 genomes]
rs6940028	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73394570	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73394572	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73394575	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73394577	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73394578	1.00[ASN][1000 genomes]
rs73394591	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73396404	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73396407	1.00[ASN][1000 genomes]
rs73396430	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73396439	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73396453	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7356832	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7357034	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73728683	0.86[ASN][1000 genomes]
rs7757501	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7771372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7771462	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7775042	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9295632	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295634	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461060	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9461061	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9461062	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9461063	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9461064	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9461065	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9461067	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461068	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461069	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9461071	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467284	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9467285	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9467286	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9467288	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9467289	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9467290	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9467291	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9467292	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9467293	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9467294	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9467295	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9467296	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9467297	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9467303	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467304	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467305	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467309	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467311	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467312	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467316	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467318	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467319	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830609	chr6:24712086-24896647	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv428474	chr6:24714157-24797977	Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv5227	chr6:24774149-24824012	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24774200-24776600	Active TSS	Fetal Brain Female	brain
2	chr6:24774200-24777000	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr6:24774200-24778200	Active TSS	K562	blood
4	chr6:24774400-24776600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr6:24774400-24776600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:24774400-24776600	Active TSS	Fetal Intestine Small	intestine
7	chr6:24774400-24776600	Active TSS	Thymus	Thymus
8	chr6:24774400-24776800	Active TSS	Brain Hippocampus Middle	brain
9	chr6:24774400-24776800	Active TSS	Colonic Mucosa	Colon
10	chr6:24774400-24777000	Active TSS	Brain Germinal Matrix	brain
11	chr6:24774400-24777200	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr6:24774400-24778400	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr6:24774600-24776600	Active TSS	H1 Cell Line	embryonic stem cell
14	chr6:24774600-24776600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr6:24774600-24776600	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr6:24774600-24776600	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr6:24774600-24776600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr6:24774600-24776600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr6:24774600-24776600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:24774600-24776600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
21	chr6:24774600-24776600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr6:24774600-24776600	Active TSS	Primary T killer memory cells from peripheral blood	blood
23	chr6:24774600-24776600	Active TSS	Muscle Satellite Cultured Cells	--
24	chr6:24774600-24776600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr6:24774600-24776600	Active TSS	Brain Anterior Caudate	brain
26	chr6:24774600-24776600	Active TSS	HMEC	breast
27	chr6:24774600-24776600	Active TSS	NHDF-Ad	bronchial
28	chr6:24774600-24776600	Active TSS	NHEK	skin
29	chr6:24774600-24776600	Active TSS	NHLF	lung
30	chr6:24774600-24776600	Active TSS	Osteobl	bone
31	chr6:24774600-24776800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr6:24774600-24776800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr6:24774600-24776800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr6:24774600-24776800	Active TSS	Brain Angular Gyrus	brain
35	chr6:24774600-24776800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr6:24774600-24777000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr6:24774600-24777000	Active TSS	H9 Cell Line	embryonic stem cell
38	chr6:24774600-24777000	Active TSS	Brain Inferior Temporal Lobe	brain
39	chr6:24774600-24777000	Active TSS	Rectal Smooth Muscle	rectum
40	chr6:24774600-24777000	Active TSS	HSMM	muscle
41	chr6:24774600-24777200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr6:24774600-24777200	Active TSS	Fetal Kidney	kidney
43	chr6:24774600-24777600	Active TSS	NH-A	brain
44	chr6:24774600-24778000	Active TSS	A549	lung
45	chr6:24774600-24779200	Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr6:24774600-24780400	Active TSS	Fetal Stomach	stomach
47	chr6:24774800-24776600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr6:24774800-24776600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr6:24774800-24776600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr6:24774800-24776600	Active TSS	Gastric	stomach

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