Variant report

Variant	rs3887175
Chromosome Location	chr5:59790456-59790457
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10516154	1.00[ASN][1000 genomes]
rs11746901	0.83[CEU][hapmap]
rs11948687	0.83[CEU][hapmap]
rs11957512	1.00[ASN][1000 genomes]
rs11960912	1.00[ASN][1000 genomes]
rs12188950	0.83[CEU][hapmap]
rs16878190	1.00[ASN][1000 genomes]
rs16878304	1.00[ASN][1000 genomes]
rs2061252	1.00[ASN][1000 genomes]
rs2061254	1.00[ASN][1000 genomes]
rs2409763	1.00[ASN][1000 genomes]
rs2441051	1.00[ASN][1000 genomes]
rs2441052	1.00[ASN][1000 genomes]
rs2591635	1.00[ASN][1000 genomes]
rs2606688	1.00[ASN][1000 genomes]
rs286150	1.00[ASN][1000 genomes]
rs286151	1.00[ASN][1000 genomes]
rs286152	1.00[ASN][1000 genomes]
rs286157	1.00[ASN][1000 genomes]
rs286159	1.00[ASN][1000 genomes]
rs3857237	1.00[ASN][1000 genomes]
rs3909458	1.00[ASN][1000 genomes]
rs6872509	1.00[ASN][1000 genomes]
rs7719095	0.83[CEU][hapmap]
rs7728865	1.00[ASN][1000 genomes]
rs9686946	1.00[ASN][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	nsv1025856	chr5:59188419-59928852	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv598288	chr5:59627555-60003460	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1018614	chr5:59708223-59910308	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv881711	chr5:59724947-59890278	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv598297	chr5:59734004-59862453	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59782000-59801000	Weak transcription	Fetal Brain Male	brain
2	chr5:59784200-59790600	Weak transcription	Brain Anterior Caudate	brain
3	chr5:59784600-59791200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr5:59784600-59791800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr5:59784600-59794200	Weak transcription	Gastric	stomach
6	chr5:59784800-59793600	Weak transcription	Colon Smooth Muscle	Colon
7	chr5:59785200-59791800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr5:59785200-59793400	Weak transcription	Fetal Stomach	stomach
9	chr5:59785800-59791000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr5:59786000-59790800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr5:59787200-59793400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr5:59787600-59791200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr5:59788800-59791800	Enhancers	HepG2	liver
14	chr5:59788800-59792600	Enhancers	A549	lung
15	chr5:59789000-59791400	Enhancers	Primary B cells from cord blood	blood
16	chr5:59789400-59791400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr5:59789400-59791600	Enhancers	Primary B cells from peripheral blood	blood
18	chr5:59789400-59793800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr5:59789600-59791200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr5:59789600-59791800	Enhancers	Muscle Satellite Cultured Cells	--
21	chr5:59789600-59794000	Weak transcription	NHEK	skin
22	chr5:59789600-59795400	Weak transcription	Aorta	Aorta
23	chr5:59789800-59790800	Enhancers	Brain Angular Gyrus	brain
24	chr5:59789800-59793600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr5:59790000-59792000	Enhancers	Brain Hippocampus Middle	brain
26	chr5:59790000-59795000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr5:59790200-59790600	Flanking Active TSS	GM12878-XiMat	blood
28	chr5:59790200-59791200	Weak transcription	HMEC	breast
29	chr5:59790200-59791400	Weak transcription	Osteobl	bone
30	chr5:59790200-59793400	Weak transcription	Stomach Smooth Muscle	stomach
31	chr5:59790200-59794200	Enhancers	Brain Substantia Nigra	brain
32	chr5:59790400-59791000	Weak transcription	Brain Cingulate Gyrus	brain
33	chr5:59790400-59794800	Weak transcription	HUES48 Cell Line	embryonic stem cell

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