Variant report

Variant	rs921599
Chromosome Location	chr2:20791125-20791126
allele	A/G
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:5)
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	chr2:20790156-20791282	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	HEY1	chr2:20790965-20791325	HepG2	liver:	n/a	n/a
6	POLR2A	chr2:20790907-20792069	HepG2	liver:	n/a	n/a
7	POLR2A	chr2:20788190-20791944	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:20644797..20655251-chr2:20787626..20802274,53	MCF-7	breast:
2	chr2:20790147..20792298-chr2:20794346..20796797,2	K562	blood:
3	chr2:20783982..20787771-chr2:20790367..20794656,9	K562	blood:
4	chr2:20786032..20787852-chr2:20789540..20791867,2	K562	blood:
5	chr2:20644186..20651576-chr2:20790196..20799394,18	MCF-7	breast:

No data

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

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10153843	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10166792	0.87[JPT][hapmap]
rs10177787	0.80[JPT][hapmap]
rs10177834	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]
rs10195324	0.82[JPT][hapmap]
rs10195722	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs11096679	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[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];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12472478	0.86[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap]
rs12621527	0.81[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs13013281	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13031724	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.91[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];1.00[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	0.86[JPT][hapmap]
rs2882036	0.82[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];0.95[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57734601	0.85[ASN][1000 genomes]
rs6712435	0.95[AFR][1000 genomes];1.00[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];0.94[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];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs766474	0.81[JPT][hapmap]

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	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
5	nsv581167	chr2:20791125-20827846	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs921599		cis	Lymphoblastoid	GTEx

Chromatin state (count:77 , 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	chr2:20785800-20793000	Weak transcription	Gastric	stomach
4	chr2:20785800-20794600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:20785800-20795200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr2:20785800-20796000	Weak transcription	Aorta	Aorta
7	chr2:20786000-20792200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:20786000-20792800	Weak transcription	Colonic Mucosa	Colon
9	chr2:20786000-20793000	Weak transcription	Brain Hippocampus Middle	brain
10	chr2:20786000-20794200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr2:20786000-20795200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr2:20786200-20797600	Weak transcription	Psoas Muscle	Psoas
13	chr2:20786800-20793400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr2:20787200-20800200	Enhancers	Right Ventricle	heart
15	chr2:20787400-20792800	Weak transcription	Fetal Kidney	kidney
16	chr2:20787400-20794800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr2:20788200-20792000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
18	chr2:20788400-20791200	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr2:20788400-20791400	Enhancers	Right Atrium	heart
20	chr2:20788400-20791800	Enhancers	Left Ventricle	heart
21	chr2:20788400-20794200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr2:20788400-20794200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr2:20788600-20791600	Enhancers	Muscle Satellite Cultured Cells	--
24	chr2:20788800-20791400	Enhancers	Fetal Muscle Leg	muscle
25	chr2:20788800-20791400	Enhancers	Fetal Stomach	stomach
26	chr2:20788800-20791400	Enhancers	NHDF-Ad	bronchial
27	chr2:20788800-20791600	Enhancers	HSMM	muscle
28	chr2:20789000-20791400	Enhancers	NHLF	lung
29	chr2:20789000-20794000	Enhancers	NHEK	skin
30	chr2:20789000-20798200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:20789200-20791400	Enhancers	HSMMtube	muscle
32	chr2:20789200-20797000	Enhancers	Spleen	Spleen
33	chr2:20789200-20800400	Enhancers	Placenta	Placenta
34	chr2:20789400-20791200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:20789400-20791800	Weak transcription	K562	blood
36	chr2:20789400-20795400	Weak transcription	Duodenum Mucosa	Duodenum
37	chr2:20789600-20792800	Weak transcription	HUVEC	blood vessel
38	chr2:20790000-20791200	Enhancers	Esophagus	oesophagus
39	chr2:20790000-20792800	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr2:20790200-20791200	Enhancers	Fetal Heart	heart
41	chr2:20790200-20791800	Enhancers	Ovary	ovary
42	chr2:20790200-20797800	Enhancers	Fetal Intestine Large	intestine
43	chr2:20790400-20791200	Enhancers	Colon Smooth Muscle	Colon
44	chr2:20790400-20791400	Flanking Active TSS	Liver	Liver
45	chr2:20790400-20791400	Enhancers	Brain Germinal Matrix	brain
46	chr2:20790400-20791400	Enhancers	Fetal Lung	lung
47	chr2:20790400-20791400	Enhancers	Rectal Smooth Muscle	rectum
48	chr2:20790400-20791600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr2:20790400-20792400	Weak transcription	A549	lung
50	chr2:20790400-20793600	Enhancers	Fetal Intestine Small	intestine

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