Variant report

Variant	rs10498795
Chromosome Location	chr6:53707423-53707424
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1543356	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs16884427	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17748452	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2223617	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2473599	0.82[AMR][1000 genomes]
rs2473603	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2494087	0.84[AMR][1000 genomes]
rs2494090	0.82[AMR][1000 genomes]
rs2820217	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2820218	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4077760	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs4131378	0.82[EUR][1000 genomes]
rs4272222	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4276504	1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4357137	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4380749	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4397225	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4476827	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4580851	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6905927	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6908101	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6919924	0.85[EUR][1000 genomes]
rs6925165	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs761135	0.89[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs7752696	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9464005	0.80[AMR][1000 genomes]
rs9474672	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv830664	chr6:53698021-53825270	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53680400-53721600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:53684000-53710200	Weak transcription	Primary T cells from cord blood	blood
3	chr6:53693400-53720000	Weak transcription	Left Ventricle	heart
4	chr6:53694000-53708400	Weak transcription	Fetal Thymus	thymus
5	chr6:53695000-53710000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr6:53695000-53719800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr6:53695000-53743200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:53696400-53708400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr6:53697200-53718600	Weak transcription	Duodenum Mucosa	Duodenum
10	chr6:53698000-53715600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr6:53699400-53709200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr6:53700400-53709200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:53703000-53708600	Weak transcription	Gastric	stomach
14	chr6:53703000-53718600	Weak transcription	Pancreas	Pancrea
15	chr6:53703200-53710400	Weak transcription	HUVEC	blood vessel
16	chr6:53703200-53720000	Weak transcription	HSMMtube	muscle
17	chr6:53703200-53720200	Weak transcription	Aorta	Aorta
18	chr6:53703200-53726400	Weak transcription	Fetal Stomach	stomach
19	chr6:53703400-53710200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr6:53703600-53710600	Weak transcription	Brain Hippocampus Middle	brain
21	chr6:53703800-53717200	Weak transcription	Primary hematopoietic stem cells	blood
22	chr6:53703800-53727600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr6:53704000-53708600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr6:53704400-53710600	Weak transcription	Colon Smooth Muscle	Colon
25	chr6:53704600-53710800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr6:53704800-53711600	Weak transcription	Brain Germinal Matrix	brain
27	chr6:53705400-53708000	Weak transcription	HepG2	liver
28	chr6:53705400-53718800	Weak transcription	NHEK	skin
29	chr6:53706000-53708600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr6:53706000-53708600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:53706000-53708600	Weak transcription	Thymus	Thymus
32	chr6:53706000-53709400	Weak transcription	Primary B cells from cord blood	blood
33	chr6:53706000-53709400	Weak transcription	Fetal Intestine Small	intestine
34	chr6:53706000-53710400	Weak transcription	Brain Substantia Nigra	brain
35	chr6:53706000-53720200	Weak transcription	Esophagus	oesophagus
36	chr6:53706000-53722400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr6:53706200-53712200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr6:53706200-53722000	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr6:53706400-53709000	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr6:53706400-53714400	Weak transcription	Fetal Muscle Trunk	muscle
41	chr6:53706400-53720200	Weak transcription	Fetal Muscle Leg	muscle
42	chr6:53706800-53710600	Enhancers	Dnd41	blood
43	chr6:53707000-53708600	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr6:53707200-53707600	Enhancers	Placenta Amnion	Placenta Amnion
45	chr6:53707200-53710400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr6:53707400-53707600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr6:53707400-53707800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr6:53707400-53707800	Enhancers	Brain Angular Gyrus	brain
49	chr6:53707400-53708400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr6:53707400-53709000	Weak transcription	Brain Anterior Caudate	brain

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