Variant report

Variant	rs2519104
Chromosome Location	chr9:136805973-136805974
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr9:136805959-136806148	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr9:136805733-136805977	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
VAV2	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs2073885	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2077384	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2263807	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2428004	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2519102	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.99[ASN][1000 genomes]
rs2519103	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2519106	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2519107	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2519108	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2519109	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2519111	0.92[CEU][hapmap]
rs2519112	0.91[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2519799	0.82[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2519802	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2519803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2519804	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2519805	1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2789848	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2789850	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2789851	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2789852	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2810530	0.99[ASN][1000 genomes]
rs2810531	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2810532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2810533	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2810534	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs886018	0.91[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894123	chr9:136682408-136852501	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv894124	chr9:136716399-136870787	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv894125	chr9:136723520-136931957	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv894127	chr9:136747832-136811772	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv894128	chr9:136753246-136906752	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv1046310	chr9:136762829-136872226	Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv894130	chr9:136767346-136906752	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS 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	25 gene(s)	inside rSNPs	diseases
8	nsv615741	chr9:136785840-136807283	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv831748	chr9:136788484-136944326	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
10	nsv894131	chr9:136792765-136906752	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:136753000-136813200	Weak transcription	Aorta	Aorta
2	chr9:136782000-136809000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr9:136784000-136819800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr9:136794000-136807400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr9:136795600-136808600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr9:136797800-136811000	Weak transcription	A549	lung
7	chr9:136801000-136815400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr9:136801200-136807400	Weak transcription	Brain Angular Gyrus	brain
9	chr9:136801200-136807400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr9:136801200-136807400	Weak transcription	Brain Hippocampus Middle	brain
11	chr9:136801200-136808200	Weak transcription	Esophagus	oesophagus
12	chr9:136801200-136815600	Weak transcription	Right Atrium	heart
13	chr9:136801200-136815800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr9:136801200-136820200	Weak transcription	Left Ventricle	heart
15	chr9:136801400-136809200	Weak transcription	HUVEC	blood vessel
16	chr9:136801400-136809800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr9:136801400-136810200	Weak transcription	Placenta	Placenta
18	chr9:136801400-136821200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr9:136802000-136807800	Weak transcription	Small Intestine	intestine
20	chr9:136802000-136815800	Weak transcription	Colonic Mucosa	Colon
21	chr9:136802200-136815800	Strong transcription	Fetal Intestine Small	intestine
22	chr9:136802600-136810200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr9:136802800-136816200	Weak transcription	Fetal Kidney	kidney
24	chr9:136803000-136807400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr9:136803000-136813000	Weak transcription	Fetal Lung	lung
26	chr9:136803000-136815200	Weak transcription	HSMMtube	muscle
27	chr9:136803200-136807800	Weak transcription	Fetal Brain Female	brain
28	chr9:136803200-136811200	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr9:136803200-136821200	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr9:136803400-136808600	Weak transcription	NH-A	brain
31	chr9:136803400-136809400	Weak transcription	HSMM	muscle
32	chr9:136803400-136809600	Weak transcription	NHLF	lung
33	chr9:136803400-136811000	Weak transcription	Hela-S3	cervix
34	chr9:136803600-136807200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr9:136803600-136821000	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr9:136803800-136806200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr9:136804000-136807200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr9:136804000-136807400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr9:136804000-136809200	Weak transcription	NHEK	skin
40	chr9:136804200-136807800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr9:136804200-136807800	Weak transcription	Spleen	Spleen
42	chr9:136804200-136809200	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr9:136804200-136810200	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr9:136804200-136810200	Weak transcription	Duodenum Mucosa	Duodenum
45	chr9:136804200-136810400	Weak transcription	Adipose Nuclei	Adipose
46	chr9:136804200-136813400	Weak transcription	Gastric	stomach
47	chr9:136804200-136815400	Weak transcription	Ovary	ovary
48	chr9:136804200-136815400	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr9:136804200-136819800	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr9:136804200-136820200	Weak transcription	HUES48 Cell Line	embryonic stem cell

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