Variant report

Variant	rs4865755
Chromosome Location	chr5:52291187-52291188
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:52284537..52287438-chr5:52289001..52291401,4	MCF-7	breast:
2	chr5:52288695..52291271-chr5:52292952..52294743,2	MCF-7	breast:
3	chr5:52285332..52287022-chr5:52289921..52292396,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164171	Chromatin interaction
ENSG00000249899	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10513004	1.00[ASW][hapmap];0.91[CEU][hapmap];0.91[GIH][hapmap];0.81[LWK][hapmap];0.80[MKK][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap];0.80[EUR][1000 genomes]
rs10940280	0.91[CEU][hapmap];0.80[YRI][hapmap];0.80[EUR][1000 genomes]
rs11738606	0.81[EUR][1000 genomes]
rs11739571	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11742694	0.85[EUR][1000 genomes]
rs11742813	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11748504	1.00[ASW][hapmap];0.91[CEU][hapmap];0.84[GIH][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs11749081	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11750600	1.00[JPT][hapmap]
rs12186544	0.82[AFR][1000 genomes]
rs13156420	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs13165509	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs13179969	0.86[CEU][hapmap]
rs13180488	0.81[EUR][1000 genomes]
rs1421943	0.92[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1592795	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3212383	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.95[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3212414	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3212656	0.92[EUR][1000 genomes]
rs34288275	0.81[EUR][1000 genomes]
rs34352729	0.85[EUR][1000 genomes]
rs34512129	0.92[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs34865297	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs35597318	0.92[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs35657730	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs35862618	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs35926366	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3776790	0.88[AMR][1000 genomes]
rs6859171	1.00[ASW][hapmap];0.82[CEU][hapmap];0.91[GIH][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap]
rs7702766	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7713782	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7735277	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9791046	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4865755	ITGA2	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52286200-52295400	Weak transcription	Pancreas	Pancrea
2	chr5:52286200-52300400	Weak transcription	Gastric	stomach
3	chr5:52286200-52303400	Weak transcription	Small Intestine	intestine
4	chr5:52286200-52313600	Weak transcription	Lung	lung
5	chr5:52286600-52292000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr5:52286600-52292600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr5:52286600-52293400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr5:52286600-52300000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr5:52286600-52302400	Weak transcription	Fetal Stomach	stomach
10	chr5:52286800-52294400	Weak transcription	Osteobl	bone
11	chr5:52286800-52298800	Weak transcription	Fetal Intestine Large	intestine
12	chr5:52287000-52292200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr5:52287000-52293000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr5:52287000-52293400	Weak transcription	Fetal Intestine Small	intestine
15	chr5:52287000-52299400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr5:52287200-52292600	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr5:52287200-52293200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr5:52287200-52293400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr5:52287200-52293600	Weak transcription	Fetal Kidney	kidney
20	chr5:52288000-52292400	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
21	chr5:52288800-52292000	Enhancers	NHDF-Ad	bronchial
22	chr5:52289000-52291600	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
23	chr5:52289200-52311600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr5:52289400-52292000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr5:52289400-52295600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr5:52290000-52292800	Enhancers	Brain Anterior Caudate	brain
27	chr5:52290000-52299800	Weak transcription	NH-A	brain
28	chr5:52290200-52291600	Enhancers	Hela-S3	cervix
29	chr5:52290400-52291600	Genic enhancers	NHEK	skin
30	chr5:52290600-52291800	Transcr. at gene 5' and 3'	HepG2	liver
31	chr5:52290600-52292400	Enhancers	Brain Angular Gyrus	brain
32	chr5:52290600-52294400	Weak transcription	NHLF	lung
33	chr5:52290800-52291200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr5:52290800-52291600	Enhancers	Spleen	Spleen
35	chr5:52290800-52292200	Genic enhancers	HMEC	breast
36	chr5:52290800-52293000	Enhancers	Brain Hippocampus Middle	brain
37	chr5:52290800-52293200	Enhancers	Brain Cingulate Gyrus	brain
38	chr5:52290800-52293200	Weak transcription	HUVEC	blood vessel
39	chr5:52291000-52291200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr5:52291000-52291200	Enhancers	Brain Substantia Nigra	brain
41	chr5:52291000-52291600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr5:52291000-52291600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr5:52291000-52291800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr5:52291000-52292400	Enhancers	Esophagus	oesophagus
45	chr5:52291000-52292800	Enhancers	A549	lung
46	chr5:52291000-52295600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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