Variant report

Variant	rs6722960
Chromosome Location	chr2:20788701-20788702
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:20788526-20788706	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:20788236-20791253	HepG2	liver:	n/a	n/a
3	POLR2A	chr2:20788250-20789585	HepG2	liver:	n/a	n/a
4	HEY1	chr2:20788217-20791446	HepG2	liver:	n/a	n/a
5	POLR2A	chr2:20788430-20789515	HepG2	liver:	n/a	n/a
6	POLR2A	chr2:20788545-20789591	HepG2	liver:	n/a	n/a
7	POLR2A	chr2:20788190-20791944	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:20644797..20655251-chr2:20787626..20802274,53	MCF-7	breast:
2	chr2:20788464..20790757-chr2:20791500..20793980,2	MCF-7	breast:
3	chr2:20787740..20790180-chr2:20814969..20816900,2	K562	blood:
4	chr2:20778568..20780393-chr2:20788647..20790853,2	K562	blood:
5	chr2:20648553..20650880-chr2:20787969..20789979,2	MCF-7	breast:
6	chr2:20773082..20775032-chr2:20787909..20789864,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000269976	TF binding region
ENSG00000228950	Chromatin interaction
ENSG00000143878	Chromatin interaction
ENSG00000231948	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10153843	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10166792	0.82[JPT][hapmap]
rs10177787	0.80[JPT][hapmap]
rs10177834	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10195324	0.82[JPT][hapmap]
rs10195722	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs11096679	0.94[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11885969	0.94[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12472478	0.87[CEU][hapmap];0.86[CHB][hapmap]
rs12621527	0.82[CEU][hapmap];0.86[CHB][hapmap]
rs13013281	0.88[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13031724	0.88[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13032956	0.94[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1466200	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16987857	0.82[JPT][hapmap]
rs2882035	0.81[JPT][hapmap]
rs4666429	0.82[JPT][hapmap]
rs4666430	0.81[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs4666431	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs4666436	0.88[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57734601	0.87[ASN][1000 genomes]
rs6712435	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6715159	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs921599	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833537	chr2:20630092-20826816	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv833548	chr2:20682073-20864078	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1012037	chr2:20770850-20824893	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv535598	chr2:20770850-20824893	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6722960		cis	Lymphoblastoid	GTEx
rs6722960	hmm27769	cis	multi-tissue	Pritchard

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20784600-20794200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr2:20785000-20788800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr2:20785000-20796000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr2:20785200-20788800	Weak transcription	HSMM	muscle
5	chr2:20785200-20789000	Weak transcription	NHEK	skin
6	chr2:20785200-20789200	Weak transcription	Osteobl	bone
7	chr2:20785400-20789200	Weak transcription	HMEC	breast
8	chr2:20785400-20789200	Weak transcription	HSMMtube	muscle
9	chr2:20785400-20789400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr2:20785600-20788800	Weak transcription	NH-A	brain
11	chr2:20785600-20790200	Weak transcription	Fetal Intestine Large	intestine
12	chr2:20785800-20789800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:20785800-20790200	Weak transcription	Fetal Heart	heart
14	chr2:20785800-20790600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr2:20785800-20793000	Weak transcription	Gastric	stomach
16	chr2:20785800-20794600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:20785800-20795200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr2:20785800-20796000	Weak transcription	Aorta	Aorta
19	chr2:20786000-20788800	Weak transcription	Lung	lung
20	chr2:20786000-20789200	Weak transcription	Spleen	Spleen
21	chr2:20786000-20789200	Weak transcription	A549	lung
22	chr2:20786000-20789400	Weak transcription	Esophagus	oesophagus
23	chr2:20786000-20790400	Weak transcription	Liver	Liver
24	chr2:20786000-20790400	Weak transcription	Fetal Lung	lung
25	chr2:20786000-20790400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr2:20786000-20790600	Weak transcription	Brain Anterior Caudate	brain
27	chr2:20786000-20790800	Weak transcription	Pancreas	Pancrea
28	chr2:20786000-20792200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr2:20786000-20792800	Weak transcription	Colonic Mucosa	Colon
30	chr2:20786000-20793000	Weak transcription	Brain Hippocampus Middle	brain
31	chr2:20786000-20794200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:20786000-20795200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr2:20786200-20788800	Weak transcription	Stomach Smooth Muscle	stomach
34	chr2:20786200-20789000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr2:20786200-20789000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr2:20786200-20789000	Weak transcription	NHLF	lung
37	chr2:20786200-20789200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr2:20786200-20789200	Weak transcription	Placenta	Placenta
39	chr2:20786200-20789200	Weak transcription	HUVEC	blood vessel
40	chr2:20786200-20790200	Weak transcription	Ovary	ovary
41	chr2:20786200-20790400	Weak transcription	Colon Smooth Muscle	Colon
42	chr2:20786200-20790400	Weak transcription	Fetal Intestine Small	intestine
43	chr2:20786200-20797600	Weak transcription	Psoas Muscle	Psoas
44	chr2:20786400-20789200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr2:20786600-20788800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr2:20786800-20788800	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr2:20786800-20788800	Weak transcription	Duodenum Mucosa	Duodenum
48	chr2:20786800-20788800	Weak transcription	NHDF-Ad	bronchial
49	chr2:20786800-20793400	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr2:20787200-20800200	Enhancers	Right Ventricle	heart

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