Variant report

Variant	rs4580851
Chromosome Location	chr6:53693186-53693187
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10498795	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1543356	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs16884427	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17748452	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2223617	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2473603	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2494087	0.83[AMR][1000 genomes]
rs2820217	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs2820218	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4077760	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[EUR][1000 genomes]
rs4131378	0.82[EUR][1000 genomes]
rs4272222	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4276504	1.00[CHB][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4357137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4380749	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4397225	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4476827	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6905927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6908101	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6919924	0.85[EUR][1000 genomes]
rs6925165	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs761135	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs7752696	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9474672	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1021506	chr6:53600338-53770482	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53670800-53693200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr6:53676200-53697800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr6:53680400-53721600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:53680600-53694400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr6:53684000-53694000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr6:53684000-53710200	Weak transcription	Primary T cells from cord blood	blood
7	chr6:53684600-53697000	Enhancers	Brain Substantia Nigra	brain
8	chr6:53687600-53702000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:53688000-53694600	Weak transcription	Fetal Muscle Leg	muscle
10	chr6:53689400-53696400	Enhancers	Stomach Mucosa	stomach
11	chr6:53689400-53699400	Enhancers	Fetal Intestine Large	intestine
12	chr6:53689600-53694400	Enhancers	HepG2	liver
13	chr6:53689600-53695400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr6:53689800-53693400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:53689800-53693400	Enhancers	Small Intestine	intestine
16	chr6:53689800-53694000	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr6:53689800-53695000	Enhancers	HMEC	breast
18	chr6:53689800-53695200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:53689800-53697200	Enhancers	Colon Smooth Muscle	Colon
20	chr6:53690000-53695400	Enhancers	Brain Cingulate Gyrus	brain
21	chr6:53690000-53699000	Enhancers	Fetal Intestine Small	intestine
22	chr6:53690200-53695000	Enhancers	Brain Hippocampus Middle	brain
23	chr6:53690200-53695600	Enhancers	NHEK	skin
24	chr6:53690400-53697200	Enhancers	Brain Anterior Caudate	brain
25	chr6:53690800-53695200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr6:53691200-53697800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr6:53691400-53693200	Enhancers	Hela-S3	cervix
28	chr6:53691400-53695000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr6:53691400-53697400	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr6:53691600-53693600	Enhancers	Muscle Satellite Cultured Cells	--
31	chr6:53691600-53693600	Enhancers	NHLF	lung
32	chr6:53691800-53693400	Enhancers	HUVEC	blood vessel
33	chr6:53691800-53695200	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr6:53692000-53693800	Enhancers	Brain Angular Gyrus	brain
35	chr6:53692000-53694400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr6:53692000-53696000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr6:53692200-53693400	Enhancers	Esophagus	oesophagus
38	chr6:53692200-53693400	Enhancers	HSMM	muscle
39	chr6:53692200-53693400	Enhancers	Osteobl	bone
40	chr6:53692200-53694000	Enhancers	Fetal Thymus	thymus
41	chr6:53692200-53694000	Enhancers	Right Atrium	heart
42	chr6:53692400-53693200	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr6:53692400-53693200	Enhancers	A549	lung
44	chr6:53692400-53693400	Enhancers	Left Ventricle	heart
45	chr6:53692400-53693400	Enhancers	Pancreas	Pancrea
46	chr6:53692400-53693400	Enhancers	Thymus	Thymus
47	chr6:53692400-53694000	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr6:53692400-53694000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr6:53692400-53694400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr6:53692400-53695000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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