Variant report

Variant	rs988658
Chromosome Location	chr5:57074790-57074791
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1016458	0.86[CHB][hapmap]
rs11738352	0.86[CHB][hapmap]
rs11749778	0.86[CHB][hapmap]
rs12519846	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1347072	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1347073	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1432477	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1432480	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1432481	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1476938	0.86[CHB][hapmap]
rs1816391	0.83[ASN][1000 genomes]
rs1835876	0.83[ASN][1000 genomes]
rs2053013	0.83[ASN][1000 genomes]
rs2215813	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2408851	0.81[CEU][hapmap];0.86[CHB][hapmap]
rs2539731	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs2539732	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2539734	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs2568533	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2568534	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2568535	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2568536	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2898030	0.83[ASN][1000 genomes]
rs2898031	0.81[ASN][1000 genomes]
rs35483666	0.83[ASN][1000 genomes]
rs4700229	0.83[ASN][1000 genomes]
rs4700230	0.83[ASN][1000 genomes]
rs6887425	0.85[CHB][hapmap]
rs6892809	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs757635	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs854025	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs854026	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs854027	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs854030	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs854032	0.99[ASN][1000 genomes]
rs854034	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs887868	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs987671	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525330	chr5:56931673-57320343	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv2756302	chr5:56978143-57180143	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv830310	chr5:56989346-57176006	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv2763454	chr5:57006531-57161140	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57062200-57075000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr5:57065400-57076000	Weak transcription	Aorta	Aorta
3	chr5:57071200-57075000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr5:57071200-57076400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr5:57071800-57076600	Enhancers	Fetal Lung	lung
6	chr5:57072200-57075400	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr5:57072400-57074800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:57072400-57076400	Enhancers	Osteobl	bone
9	chr5:57072400-57076600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr5:57072600-57074800	Weak transcription	Brain Germinal Matrix	brain
11	chr5:57072600-57074800	Weak transcription	Fetal Muscle Leg	muscle
12	chr5:57072600-57079600	Weak transcription	Ovary	ovary
13	chr5:57072800-57075000	Weak transcription	HMEC	breast
14	chr5:57072800-57075600	Weak transcription	NHEK	skin
15	chr5:57073000-57075400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr5:57073000-57075600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr5:57073000-57075800	Enhancers	Liver	Liver
18	chr5:57073200-57075600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr5:57073200-57076000	Enhancers	HUVEC	blood vessel
20	chr5:57073200-57077000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr5:57073400-57074800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr5:57073400-57075600	Weak transcription	HSMMtube	muscle
23	chr5:57073400-57076600	Enhancers	A549	lung
24	chr5:57073600-57074800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr5:57073600-57075400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr5:57073800-57076600	Enhancers	Fetal Intestine Large	intestine
27	chr5:57074000-57075000	Enhancers	Pancreas	Pancrea
28	chr5:57074000-57076600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr5:57074000-57077000	Enhancers	Fetal Heart	heart
30	chr5:57074200-57074800	Enhancers	Duodenum Mucosa	Duodenum
31	chr5:57074200-57076800	Enhancers	Fetal Intestine Small	intestine
32	chr5:57074200-57076800	Enhancers	NH-A	brain
33	chr5:57074200-57077000	Enhancers	Stomach Mucosa	stomach
34	chr5:57074600-57075000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr5:57074600-57075000	Enhancers	HepG2	liver
36	chr5:57074600-57075400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr5:57074600-57075600	Enhancers	Fetal Kidney	kidney
38	chr5:57074600-57075800	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr5:57074600-57076000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr5:57074600-57076000	Enhancers	Fetal Stomach	stomach
41	chr5:57074600-57076400	Enhancers	HSMM	muscle

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