Variant report

Variant	rs4235477
Chromosome Location	chr5:59061282-59061283
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	chr11:62608526..62609390-chr5:59060896..59061540,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000133316	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10061253	1.00[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1011644	1.00[CHB][hapmap];0.87[JPT][hapmap];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1117923	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs1370230	0.95[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.80[JPT][hapmap]
rs169869	0.83[ASN][1000 genomes]
rs17742664	1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[YRI][hapmap];0.90[ASN][1000 genomes]
rs1992112	1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs2164661	0.95[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs256348	0.81[ASW][hapmap]
rs256356	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs2938784	0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap]
rs2938785	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs2963824	0.95[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[TSI][hapmap];0.81[YRI][hapmap]
rs298058	0.95[CHB][hapmap];0.80[JPT][hapmap]
rs298059	0.81[CEU][hapmap];0.86[CHB][hapmap]
rs298061	0.95[CHB][hapmap]
rs298062	0.81[CEU][hapmap];0.86[CHB][hapmap]
rs298063	0.81[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap]
rs298067	0.90[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs298072	0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs298075	0.82[ASN][1000 genomes]
rs298083	0.82[ASN][1000 genomes]
rs298084	0.81[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap]
rs298091	0.81[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap]
rs298092	0.83[ASN][1000 genomes]
rs298093	0.95[CHB][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs298096	0.95[CHB][hapmap];0.80[JPT][hapmap];0.84[ASN][1000 genomes]
rs6450526	0.81[CEU][hapmap];0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs6450527	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.87[JPT][hapmap];0.91[YRI][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6450529	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6450531	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs6450532	0.95[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap]
rs6865459	0.87[ASN][1000 genomes]
rs6869459	0.95[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap]
rs6875753	0.90[CHB][hapmap];0.86[ASN][1000 genomes]
rs7701573	1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs7701748	1.00[CHB][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs905834	0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap]
rs965864	0.90[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	nsv881708	chr5:58869051-59093198	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1018015	chr5:58889470-59532667	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv537766	chr5:58889470-59532667	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv427720	chr5:58913581-59086987	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
5	nsv534614	chr5:58962510-59388525	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59048800-59064000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:59052600-59064200	Weak transcription	Aorta	Aorta
3	chr5:59054200-59062200	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr5:59054600-59061400	Weak transcription	Duodenum Mucosa	Duodenum
5	chr5:59055200-59061400	Weak transcription	Fetal Brain Male	brain
6	chr5:59055800-59061400	Weak transcription	Esophagus	oesophagus
7	chr5:59055800-59061800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr5:59055800-59062000	Weak transcription	Fetal Stomach	stomach
9	chr5:59055800-59063600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr5:59056800-59062200	Weak transcription	HSMM	muscle
11	chr5:59057000-59061400	Weak transcription	Fetal Kidney	kidney
12	chr5:59057000-59062000	Weak transcription	Stomach Mucosa	stomach
13	chr5:59057600-59061800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr5:59057600-59062000	Weak transcription	Small Intestine	intestine
15	chr5:59057600-59062200	Weak transcription	Fetal Intestine Small	intestine
16	chr5:59057600-59062400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr5:59057600-59062400	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr5:59057800-59061600	Weak transcription	HMEC	breast
19	chr5:59057800-59062200	Weak transcription	NH-A	brain
20	chr5:59058600-59061400	Enhancers	HUVEC	blood vessel
21	chr5:59059400-59061400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr5:59059400-59062000	Enhancers	Primary B cells from peripheral blood	blood
23	chr5:59060000-59061400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr5:59060000-59061600	Weak transcription	Fetal Lung	lung
25	chr5:59060000-59062200	Weak transcription	Fetal Intestine Large	intestine
26	chr5:59060200-59061600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr5:59060200-59061800	Transcr. at gene 5' and 3'	Hela-S3	cervix
28	chr5:59060200-59062200	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr5:59060600-59061400	Transcr. at gene 5' and 3'	A549	lung
30	chr5:59060800-59062200	Enhancers	Fetal Muscle Leg	muscle
31	chr5:59060800-59065200	Active TSS	Rectal Mucosa Donor 29	rectum
32	chr5:59061000-59061800	Enhancers	Placenta Amnion	Placenta Amnion
33	chr5:59061200-59061400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr5:59061200-59061400	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr5:59061200-59061600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr5:59061200-59061600	Flanking Active TSS	Colon Smooth Muscle	Colon
37	chr5:59061200-59061600	Flanking Active TSS	Rectal Smooth Muscle	rectum
38	chr5:59061200-59061800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
39	chr5:59061200-59062000	Enhancers	NHEK	skin

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