Variant report

Variant	rs10177834
Chromosome Location	chr2:20790512-20790513
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:20790156-20791282	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:20788236-20791253	HepG2	liver:	n/a	n/a
3	HEY1	chr2:20788217-20791446	HepG2	liver:	n/a	n/a
4	POLR2A	chr2:20789823-20791179	HepG2	liver:	n/a	n/a
5	HNF4A	chr2:20790452-20790783	HepG2	liver:	n/a	chr2:20790622-20790637
6	HEY1	chr2:20790179-20790697	HepG2	liver:	n/a	n/a
7	POLR2A	chr2:20789971-20791121	HepG2	liver:	n/a	n/a
8	POLR2A	chr2:20788190-20791944	HepG2	liver:	n/a	n/a
9	HNF4A	chr2:20790449-20790800	HepG2	liver:	n/a	chr2:20790622-20790637
10	RCOR1	chr2:20790217-20790758	HepG2	liver:	n/a	n/a

No data

(count:7 , 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	chr2:20790147..20792298-chr2:20794346..20796797,2	K562	blood:
4	chr2:20783982..20787771-chr2:20790367..20794656,9	K562	blood:
5	chr2:20786032..20787852-chr2:20789540..20791867,2	K562	blood:
6	chr2:20778568..20780393-chr2:20788647..20790853,2	K562	blood:
7	chr2:20644186..20651576-chr2:20790196..20799394,18	MCF-7	breast:

No data

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

Extended variants
information (count: 28 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10153843	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10166792	0.82[JPT][hapmap]
rs10177787	0.80[JPT][hapmap]
rs10195324	0.82[JPT][hapmap]
rs10195722	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs11096679	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11885969	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[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];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13031724	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13032956	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1466200	0.84[EUR][1000 genomes];0.98[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];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57734601	0.85[ASN][1000 genomes]
rs6712435	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6715159	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6722960	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]
rs921599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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

No data

Chromatin state (count:73 , 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	chr2:20785000-20796000	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr2:20785800-20790600	Weak transcription	Brain Cingulate Gyrus	brain
4	chr2:20785800-20793000	Weak transcription	Gastric	stomach
5	chr2:20785800-20794600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:20785800-20795200	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr2:20785800-20796000	Weak transcription	Aorta	Aorta
8	chr2:20786000-20790600	Weak transcription	Brain Anterior Caudate	brain
9	chr2:20786000-20790800	Weak transcription	Pancreas	Pancrea
10	chr2:20786000-20792200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:20786000-20792800	Weak transcription	Colonic Mucosa	Colon
12	chr2:20786000-20793000	Weak transcription	Brain Hippocampus Middle	brain
13	chr2:20786000-20794200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr2:20786000-20795200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr2:20786200-20797600	Weak transcription	Psoas Muscle	Psoas
16	chr2:20786800-20793400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr2:20787200-20800200	Enhancers	Right Ventricle	heart
18	chr2:20787400-20792800	Weak transcription	Fetal Kidney	kidney
19	chr2:20787400-20794800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr2:20787800-20790800	Weak transcription	Brain Substantia Nigra	brain
21	chr2:20788200-20792000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
22	chr2:20788400-20790800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr2:20788400-20791200	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr2:20788400-20791400	Enhancers	Right Atrium	heart
25	chr2:20788400-20791800	Enhancers	Left Ventricle	heart
26	chr2:20788400-20794200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr2:20788400-20794200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr2:20788600-20791600	Enhancers	Muscle Satellite Cultured Cells	--
29	chr2:20788800-20790800	Transcr. at gene 5' and 3'	HepG2	liver
30	chr2:20788800-20790800	Enhancers	NH-A	brain
31	chr2:20788800-20791000	Enhancers	Lung	lung
32	chr2:20788800-20791400	Enhancers	Fetal Muscle Leg	muscle
33	chr2:20788800-20791400	Enhancers	Fetal Stomach	stomach
34	chr2:20788800-20791400	Enhancers	NHDF-Ad	bronchial
35	chr2:20788800-20791600	Enhancers	HSMM	muscle
36	chr2:20789000-20791400	Enhancers	NHLF	lung
37	chr2:20789000-20794000	Enhancers	NHEK	skin
38	chr2:20789000-20798200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr2:20789200-20790600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr2:20789200-20790600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr2:20789200-20790600	Enhancers	Osteobl	bone
42	chr2:20789200-20790800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr2:20789200-20791000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr2:20789200-20791000	Enhancers	HMEC	breast
45	chr2:20789200-20791400	Enhancers	HSMMtube	muscle
46	chr2:20789200-20797000	Enhancers	Spleen	Spleen
47	chr2:20789200-20800400	Enhancers	Placenta	Placenta
48	chr2:20789400-20791200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr2:20789400-20791800	Weak transcription	K562	blood
50	chr2:20789400-20795400	Weak transcription	Duodenum Mucosa	Duodenum

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