Variant report

Variant	rs6885499
Chromosome Location	chr5:60575897-60575898
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10037643	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10052765	0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10062338	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10065444	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10071763	0.91[ASN][1000 genomes]
rs10434526	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10461467	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10471510	0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10939888	0.91[ASN][1000 genomes]
rs10939890	0.91[ASN][1000 genomes]
rs10939892	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10939893	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12189426	0.91[ASN][1000 genomes]
rs12518152	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12523278	0.83[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs12696979	0.89[ASN][1000 genomes]
rs12696980	0.91[ASN][1000 genomes]
rs13175564	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13187871	0.80[EUR][1000 genomes]
rs34439016	0.95[ASN][1000 genomes]
rs35310874	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4129437	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4400074	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4441832	0.95[ASN][1000 genomes]
rs4540126	0.91[ASN][1000 genomes]
rs4699974	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4699975	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6864367	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6867268	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6867417	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6892128	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.93[ASN][1000 genomes]
rs7448844	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7737448	0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9291718	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]

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	nsv1034038	chr5:60375328-60607654	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv1028884	chr5:60414723-60732779	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv823088	chr5:60572580-60577406	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv441955	chr5:60573147-60576860	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60564600-60576000	Weak transcription	Psoas Muscle	Psoas
2	chr5:60567800-60577200	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr5:60571200-60576600	Weak transcription	Pancreas	Pancrea
4	chr5:60571800-60583800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr5:60572000-60577000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr5:60572000-60582400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr5:60573400-60586600	Weak transcription	Esophagus	oesophagus
8	chr5:60573400-60594800	Weak transcription	Right Atrium	heart
9	chr5:60573600-60576000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr5:60573600-60576000	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr5:60573600-60576000	Weak transcription	Colon Smooth Muscle	Colon
12	chr5:60573600-60576000	Weak transcription	Fetal Lung	lung
13	chr5:60573600-60576000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr5:60573600-60576000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr5:60573600-60576000	Weak transcription	Stomach Mucosa	stomach
16	chr5:60573600-60576000	Weak transcription	GM12878-XiMat	blood
17	chr5:60573600-60576200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:60573600-60576200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr5:60573600-60576200	Weak transcription	Brain Substantia Nigra	brain
20	chr5:60573800-60576000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr5:60573800-60576200	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr5:60573800-60576600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr5:60574000-60576200	Weak transcription	Brain Hippocampus Middle	brain
24	chr5:60574000-60576600	Weak transcription	Duodenum Mucosa	Duodenum
25	chr5:60574000-60585400	Weak transcription	Spleen	Spleen
26	chr5:60574600-60576800	Enhancers	Small Intestine	intestine
27	chr5:60574600-60577600	Enhancers	Monocytes-CD14+_RO01746	blood
28	chr5:60575200-60577400	Enhancers	Fetal Heart	heart
29	chr5:60575400-60576000	Enhancers	NHEK	skin
30	chr5:60575400-60576800	Enhancers	Pancreatic Islets	Pancreatic Islet
31	chr5:60575400-60577400	Enhancers	Fetal Intestine Small	intestine
32	chr5:60575400-60577400	Enhancers	HMEC	breast
33	chr5:60575400-60577800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr5:60575400-60577800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr5:60575400-60577800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr5:60575600-60576000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr5:60575600-60576000	Enhancers	NH-A	brain
38	chr5:60575600-60576800	Enhancers	Stomach Smooth Muscle	stomach
39	chr5:60575600-60577000	Enhancers	NHLF	lung
40	chr5:60575600-60577200	Enhancers	Primary B cells from peripheral blood	blood
41	chr5:60575600-60577200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr5:60575600-60577200	Enhancers	Muscle Satellite Cultured Cells	--
43	chr5:60575600-60577200	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr5:60575600-60577200	Enhancers	HSMM	muscle
45	chr5:60575600-60577200	Enhancers	Osteobl	bone
46	chr5:60575600-60577400	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr5:60575600-60577400	Enhancers	Brain Germinal Matrix	brain
48	chr5:60575600-60577400	Enhancers	Fetal Intestine Large	intestine
49	chr5:60575600-60577800	Enhancers	HUVEC	blood vessel
50	chr5:60575800-60576600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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