Variant report

Variant	rs6743991
Chromosome Location	chr2:46583235-46583236
allele	A/C
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	POLR2A	chr2:46578006-46586107	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:46582963-46583278	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr2:46583179-46583790	K562	blood:	n/a	n/a
4	POLR2A	chr2:46582287-46583854	A549	lung:	n/a	n/a
5	POLR2A	chr2:46583049-46583799	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr2:46583036-46583242	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
EPAS1	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10191091	0.85[CEU][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11675232	0.85[CEU][hapmap]
rs11675441	0.81[CEU][hapmap]
rs11678465	0.81[CEU][hapmap]
rs11692911	0.85[CEU][hapmap]
rs11694193	0.81[CEU][hapmap]
rs1530631	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1530633	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1562452	0.89[CEU][hapmap];0.85[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1562453	0.96[CEU][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2881324	0.85[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]
rs3768730	0.85[CEU][hapmap];0.89[MEX][hapmap];0.80[AMR][1000 genomes]
rs4953356	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4953358	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4953359	1.00[CEU][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6544887	0.89[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6544888	0.92[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6544889	0.89[CEU][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6544890	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6707241	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6735812	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6740096	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6756667	1.00[CEU][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7586141	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7594278	0.81[CEU][hapmap]
rs7598371	0.84[CEU][hapmap]

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	nsv1012446	chr2:45921682-46737036	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv916169	chr2:46310963-46622603	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats 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	25 gene(s)	inside rSNPs	diseases
3	esv2757795	chr2:46532812-46874151	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv2759046	chr2:46532812-46874151	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6743991	EPAS1	cis	parietal	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46567400-46584600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr2:46568000-46596600	Weak transcription	Colon Smooth Muscle	Colon
3	chr2:46570200-46584800	Weak transcription	Small Intestine	intestine
4	chr2:46572000-46584600	Weak transcription	Brain Hippocampus Middle	brain
5	chr2:46572600-46590600	Strong transcription	NHEK	skin
6	chr2:46573200-46584200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:46573200-46613000	Strong transcription	Hela-S3	cervix
8	chr2:46573600-46583600	Weak transcription	Stomach Mucosa	stomach
9	chr2:46573800-46591400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:46574000-46586200	Strong transcription	Sigmoid Colon	Sigmoid Colon
11	chr2:46574000-46589200	Strong transcription	Osteobl	bone
12	chr2:46574000-46589600	Strong transcription	A549	lung
13	chr2:46574200-46589600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr2:46574200-46590600	Strong transcription	Placenta Amnion	Placenta Amnion
15	chr2:46574400-46587400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:46574400-46590400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr2:46574600-46607200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:46574800-46613000	Weak transcription	HSMM	muscle
19	chr2:46575600-46583800	Weak transcription	HSMMtube	muscle
20	chr2:46575600-46584400	Weak transcription	Brain Substantia Nigra	brain
21	chr2:46576600-46583400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:46576600-46585200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr2:46577000-46583600	Strong transcription	HepG2	liver
24	chr2:46578400-46583600	Weak transcription	Fetal Intestine Large	intestine
25	chr2:46578400-46585600	Genic enhancers	Left Ventricle	heart
26	chr2:46578600-46590400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr2:46578800-46590800	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr2:46579000-46585600	Strong transcription	Fetal Intestine Small	intestine
29	chr2:46579400-46588000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr2:46579600-46583400	Weak transcription	NHDF-Ad	bronchial
31	chr2:46579600-46583600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr2:46579600-46585400	Enhancers	Fetal Thymus	thymus
33	chr2:46579600-46587800	Weak transcription	Fetal Lung	lung
34	chr2:46580000-46583600	Weak transcription	Fetal Muscle Leg	muscle
35	chr2:46580000-46587800	Weak transcription	Fetal Muscle Trunk	muscle
36	chr2:46580000-46588600	Strong transcription	NHLF	lung
37	chr2:46580000-46589000	Strong transcription	Liver	Liver
38	chr2:46580000-46594600	Weak transcription	Psoas Muscle	Psoas
39	chr2:46580200-46585200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr2:46580200-46585600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr2:46580200-46588600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr2:46580400-46589600	Strong transcription	Duodenum Mucosa	Duodenum
43	chr2:46580600-46585600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr2:46580600-46589200	Weak transcription	Dnd41	blood
45	chr2:46580600-46589600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr2:46580600-46597200	Weak transcription	Fetal Heart	heart
47	chr2:46580800-46584000	Weak transcription	Brain Anterior Caudate	brain
48	chr2:46580800-46589800	Strong transcription	HUVEC	blood vessel
49	chr2:46581000-46583800	Weak transcription	Thymus	Thymus
50	chr2:46581000-46586200	Genic enhancers	Right Ventricle	heart

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