Variant report

Variant	rs62386577
Chromosome Location	chr6:4803142-4803143
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:4794303..4796795-chr6:4800543..4803644,3	MCF-7	breast:
2	chr6:4777710..4780092-chr6:4801744..4804702,2	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1016877	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11967994	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11968021	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1265332	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1265333	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1265334	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1265335	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17138856	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs184588	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2179269	0.83[EUR][1000 genomes]
rs2179270	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs233476	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3748078	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61610972	0.87[EUR][1000 genomes]
rs62386574	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62386575	0.88[EUR][1000 genomes]
rs62386576	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62386578	0.89[EUR][1000 genomes]
rs62386582	0.87[EUR][1000 genomes]
rs62386584	0.87[EUR][1000 genomes]
rs62386585	0.87[EUR][1000 genomes]
rs62386587	0.85[EUR][1000 genomes]
rs62386590	0.83[EUR][1000 genomes]
rs6910368	0.88[EUR][1000 genomes]
rs6918626	0.85[EUR][1000 genomes]
rs73362560	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs808593	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs808598	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs808600	0.82[EUR][1000 genomes]
rs808606	0.83[EUR][1000 genomes]
rs808607	0.83[EUR][1000 genomes]
rs808635	0.83[EUR][1000 genomes]
rs9504254	0.88[AMR][1000 genomes];1.00[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	esv3366530	chr6:4471528-4865322	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv2422499	chr6:4745428-5073222	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1015888	chr6:4787784-4883663	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4787400-4808800	Weak transcription	Aorta	Aorta
2	chr6:4790200-4803200	Weak transcription	Pancreas	Pancrea
3	chr6:4794800-4803200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:4794800-4803200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:4794800-4803600	Weak transcription	Esophagus	oesophagus
6	chr6:4794800-4804400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr6:4794800-4818800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr6:4795000-4803200	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr6:4795000-4803200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:4795000-4803200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:4795000-4806200	Weak transcription	Gastric	stomach
12	chr6:4795200-4803400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr6:4795200-4803800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr6:4795200-4806600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr6:4797400-4803200	Weak transcription	HSMM	muscle
16	chr6:4798000-4803200	Weak transcription	NHEK	skin
17	chr6:4798200-4803600	Weak transcription	Hela-S3	cervix
18	chr6:4798200-4803600	Weak transcription	NHLF	lung
19	chr6:4798400-4803200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr6:4800000-4803200	Weak transcription	Spleen	Spleen
21	chr6:4800000-4810400	Weak transcription	Fetal Intestine Small	intestine
22	chr6:4800800-4804000	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr6:4801000-4803800	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr6:4801000-4805000	Enhancers	Primary B cells from peripheral blood	blood
25	chr6:4801000-4805600	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr6:4801200-4803600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr6:4801200-4804000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr6:4801600-4803200	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr6:4801600-4804800	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr6:4801800-4803400	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr6:4801800-4803600	Enhancers	Primary T cells from cord blood	blood
32	chr6:4801800-4804000	Enhancers	Liver	Liver
33	chr6:4801800-4804000	Enhancers	Fetal Thymus	thymus
34	chr6:4801800-4804600	Enhancers	Primary T cells fromperipheralblood	blood
35	chr6:4801800-4805000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr6:4801800-4805200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr6:4801800-4805200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr6:4801800-4805200	Enhancers	Psoas Muscle	Psoas
39	chr6:4801800-4811600	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr6:4802000-4803200	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr6:4802000-4803200	Weak transcription	Brain Hippocampus Middle	brain
42	chr6:4802000-4803400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr6:4802000-4803400	Weak transcription	Colonic Mucosa	Colon
44	chr6:4802000-4803600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr6:4802000-4803800	Enhancers	Adipose Nuclei	Adipose
46	chr6:4802000-4805000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr6:4802200-4803200	Weak transcription	Duodenum Mucosa	Duodenum
48	chr6:4802200-4803200	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr6:4802200-4803400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr6:4802200-4803800	Enhancers	Duodenum Smooth Muscle	Duodenum

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