Variant report

Variant	rs2473599
Chromosome Location	chr6:53784956-53784957
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10498795	0.82[AMR][1000 genomes]
rs12196155	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1543356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16884427	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2223617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2473601	0.91[EUR][1000 genomes]
rs2473603	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2494087	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2494089	0.91[EUR][1000 genomes]
rs2494090	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2494091	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2745460	0.93[EUR][1000 genomes]
rs2820217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2820218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2894816	0.81[EUR][1000 genomes]
rs4077760	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4272222	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4276504	1.00[CHB][hapmap]
rs4357137	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4380749	0.80[EUR][1000 genomes]
rs4397225	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4476827	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6903532	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6905927	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs6908101	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6925165	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs761135	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs761136	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs763814	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7752800	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7772783	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9382261	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9382262	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9382264	0.82[EUR][1000 genomes]
rs9463996	0.97[YRI][hapmap]
rs9464005	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9474672	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[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	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:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53759200-53787600	Weak transcription	Spleen	Spleen
2	chr6:53759200-53794400	Weak transcription	Right Ventricle	heart
3	chr6:53759400-53786400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr6:53759600-53789800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:53760400-53789400	Weak transcription	Stomach Mucosa	stomach
6	chr6:53760400-53791200	Weak transcription	Hela-S3	cervix
7	chr6:53760600-53793600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr6:53761000-53785400	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr6:53761400-53787400	Weak transcription	HMEC	breast
10	chr6:53761400-53791200	Weak transcription	Colon Smooth Muscle	Colon
11	chr6:53761600-53790800	Weak transcription	Fetal Heart	heart
12	chr6:53761800-53786800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:53762000-53791200	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr6:53762000-53791600	Weak transcription	Fetal Lung	lung
15	chr6:53762200-53786800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr6:53768600-53785000	Weak transcription	Primary B cells from cord blood	blood
17	chr6:53768800-53796000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr6:53769000-53785400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:53769200-53790400	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr6:53769600-53785200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr6:53770000-53795800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr6:53770600-53787400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr6:53771200-53785000	Weak transcription	Left Ventricle	heart
24	chr6:53772000-53787600	Weak transcription	Pancreas	Pancrea
25	chr6:53772000-53803000	Weak transcription	Lung	lung
26	chr6:53776000-53786600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr6:53776000-53790600	Weak transcription	Brain Germinal Matrix	brain
28	chr6:53776200-53786400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:53776400-53786600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr6:53776600-53785200	Weak transcription	Ovary	ovary
31	chr6:53776600-53789200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr6:53776800-53791000	Weak transcription	HUVEC	blood vessel
33	chr6:53777600-53790600	Strong transcription	Fetal Thymus	thymus
34	chr6:53778000-53787800	Strong transcription	Dnd41	blood
35	chr6:53778000-53791800	Weak transcription	Small Intestine	intestine
36	chr6:53779200-53787600	Weak transcription	Aorta	Aorta
37	chr6:53779400-53787600	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr6:53779600-53785400	Weak transcription	Stomach Smooth Muscle	stomach
39	chr6:53779600-53787400	Weak transcription	Esophagus	oesophagus
40	chr6:53779600-53791400	Weak transcription	Placenta	Placenta
41	chr6:53779800-53785400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr6:53780200-53790400	Weak transcription	Gastric	stomach
43	chr6:53780600-53785000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr6:53780600-53785200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr6:53781000-53787200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr6:53781000-53789200	Weak transcription	Primary B cells from peripheral blood	blood
47	chr6:53781000-53791200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr6:53782200-53785400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr6:53782200-53787800	Weak transcription	Brain Angular Gyrus	brain
50	chr6:53782400-53789400	Weak transcription	Brain Inferior Temporal Lobe	brain

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