Variant report

Variant	rs4865756
Chromosome Location	chr5:52313564-52313565
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:52313064..52315275-chr5:52327348..52329688,2	MCF-7	breast:

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1421942	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3212391	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3212418	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212521	0.87[YRI][hapmap]
rs35235	0.83[GIH][hapmap];0.80[MEX][hapmap]
rs6450106	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462187	chr5:51758804-52333420	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv598163	chr5:51758804-52333420	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv471013	chr5:51779197-52339114	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv830296	chr5:52209528-52410253	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv880425	chr5:52291279-52345868	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4865756	ESM1	cis	parietal	SCAN
rs4865756	ITGA2	cis	multi-tissue	Pritchard
rs4865756	ITGA2	cis	Artery Tibial	GTEx

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52286200-52313600	Weak transcription	Lung	lung
2	chr5:52303400-52320400	Weak transcription	Fetal Brain Male	brain
3	chr5:52305000-52314600	Weak transcription	HUVEC	blood vessel
4	chr5:52305200-52317200	Weak transcription	A549	lung
5	chr5:52307000-52333800	Weak transcription	Gastric	stomach
6	chr5:52307800-52313800	Weak transcription	NHEK	skin
7	chr5:52308800-52313600	Enhancers	HepG2	liver
8	chr5:52310800-52315000	Enhancers	Hela-S3	cervix
9	chr5:52311000-52314200	Enhancers	Brain Hippocampus Middle	brain
10	chr5:52311400-52314000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr5:52311600-52314200	Enhancers	Brain Substantia Nigra	brain
12	chr5:52311800-52317200	Weak transcription	NHLF	lung
13	chr5:52312000-52314000	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr5:52312000-52318400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr5:52312400-52313800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr5:52312800-52313800	Enhancers	Brain Angular Gyrus	brain
17	chr5:52312800-52313800	Genic enhancers	HMEC	breast
18	chr5:52312800-52314400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr5:52312800-52315600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr5:52313000-52313600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr5:52313000-52313600	Enhancers	NH-A	brain
22	chr5:52313000-52313600	Enhancers	NHDF-Ad	bronchial
23	chr5:52313000-52314200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr5:52313200-52313600	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr5:52313200-52313800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr5:52313200-52313800	Enhancers	Brain Anterior Caudate	brain
27	chr5:52313200-52315800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr5:52313400-52313600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr5:52313400-52313600	Enhancers	Right Ventricle	heart
30	chr5:52313400-52313800	Enhancers	Brain Cingulate Gyrus	brain
31	chr5:52313400-52313800	Enhancers	Spleen	Spleen
32	chr5:52313400-52314000	Genic enhancers	Esophagus	oesophagus
33	chr5:52313400-52314400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr5:52313400-52314400	Strong transcription	Fetal Intestine Small	intestine
35	chr5:52313400-52315800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr5:52313400-52319400	Weak transcription	Muscle Satellite Cultured Cells	--

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