Variant report

Variant	rs6720394
Chromosome Location	chr2:111989372-111989373
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:111985051..111989984-chr2:111990013..111994177,5	K562	blood:

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs6705044	0.80[YRI][hapmap];0.85[AFR][1000 genomes]
rs72837843	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72837847	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72837849	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72837850	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72837868	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72950246	0.87[AFR][1000 genomes]
rs72950249	0.87[AFR][1000 genomes]
rs72950252	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874838	chr2:111376870-112046226	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv834331	chr2:111812139-112004678	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	esv1803356	chr2:111899783-112662597	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv428402	chr2:111899783-112662597	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	esv1801950	chr2:111899783-112746937	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	esv2757825	chr2:111899783-112746937	Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
7	esv2759083	chr2:111899783-112746937	Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	nsv874843	chr2:111966947-112023328	Enhancers ZNF genes & repeats Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Primary sclerosing cholangitis	21151127	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6720394	TAT	trans	parietal	SCAN
rs6720394	IL1A	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:111954800-112006800	Weak transcription	HUVEC	blood vessel
2	chr2:111975200-112008200	Weak transcription	Pancreas	Pancrea
3	chr2:111977600-112011400	Weak transcription	A549	lung
4	chr2:111980600-111993000	Weak transcription	Left Ventricle	heart
5	chr2:111980800-111993000	Weak transcription	Right Ventricle	heart
6	chr2:111983400-111989400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr2:111984000-111994000	Weak transcription	K562	blood
8	chr2:111985800-111992600	Weak transcription	HMEC	breast
9	chr2:111985800-111992800	Weak transcription	Esophagus	oesophagus
10	chr2:111985800-111993000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:111985800-112009600	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr2:111986000-111995600	Weak transcription	HepG2	liver
13	chr2:111986200-111989600	Weak transcription	HSMM	muscle
14	chr2:111986200-111989800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:111986200-111992800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:111986200-111992800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:111986200-111993000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:111986200-111993600	Weak transcription	HSMMtube	muscle
19	chr2:111986200-111995200	Weak transcription	NH-A	brain
20	chr2:111986200-111995400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr2:111986200-112004400	Weak transcription	Osteobl	bone
22	chr2:111986400-111995400	Weak transcription	NHLF	lung
23	chr2:111986400-111995800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:111986400-112004000	Weak transcription	NHDF-Ad	bronchial
25	chr2:111989200-111990000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:111989200-111990200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr2:111989200-111993800	Weak transcription	Fetal Muscle Trunk	muscle

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