Variant report

Variant	rs2053881
Chromosome Location	chr5:40983091-40983092
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	chr5:40976435..40978654-chr5:40981165..40983348,2	MCF-7	breast:
2	chr5:40982776..40984808-chr5:40985903..40987745,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112936	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1061429	0.84[CHB][hapmap]
rs10941528	0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.86[ASN][1000 genomes]
rs1138523	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1138524	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11948665	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13157656	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1501815	1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs2122568	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2167232	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2305313	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35648492	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3805217	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs3805221	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3828510	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66762907	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67313812	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6871948	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6872291	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71623870	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71623871	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71623873	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7712533	0.87[CHB][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881467	chr5:40869802-41008650	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv2757114	chr5:40874078-41009282	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv2759341	chr5:40874078-41009282	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv823055	chr5:40875708-41004839	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv35077	chr5:40875843-41000671	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv830268	chr5:40897361-41138366	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv880796	chr5:40934832-40985604	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2053881	C6	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40931200-40992200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr5:40931800-40991000	Weak transcription	Duodenum Mucosa	Duodenum
3	chr5:40960400-40989600	Weak transcription	Left Ventricle	heart
4	chr5:40968200-40990400	Weak transcription	Fetal Intestine Large	intestine
5	chr5:40972200-40984000	Weak transcription	Right Ventricle	heart
6	chr5:40975600-40985800	Weak transcription	Fetal Brain Male	brain
7	chr5:40976800-40985000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr5:40977800-40984000	Weak transcription	Fetal Intestine Small	intestine
9	chr5:40979400-40991000	Weak transcription	Fetal Kidney	kidney
10	chr5:40981000-40988800	Weak transcription	Lung	lung
11	chr5:40982000-40983600	Strong transcription	Fetal Lung	lung
12	chr5:40982000-40991800	Weak transcription	Spleen	Spleen
13	chr5:40982400-40984000	Weak transcription	Ovary	ovary
14	chr5:40982600-40983800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr5:40983000-40986200	Enhancers	HMEC	breast

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