Variant report

Variant	rs9395882
Chromosome Location	chr6:53725288-53725289
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:53719967..53722619-chr6:53723859..53726928,3	MCF-7	breast:
2	chr6:53725023..53728197-chr6:53731513..53733872,3	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10948783	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10948784	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12193567	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12194768	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12209621	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3935664	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4128619	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4236114	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4260754	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4265034	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4273680	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4331986	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4392712	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4515373	0.81[ASN][1000 genomes]
rs4583974	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4612163	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4624872	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4645423	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6458967	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6458968	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6904545	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6906921	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6907027	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6910777	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6913431	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6935621	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6935838	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7453639	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7745548	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7749635	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7749749	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7751036	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7755924	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7761285	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9296722	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9296723	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9349682	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9349683	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9349684	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9367543	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9370234	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9370237	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9370238	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9370240	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9382240	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9382242	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9382245	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9382247	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9395879	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9395880	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9395883	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9395884	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9395887	0.87[AMR][1000 genomes];0.84[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:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53695000-53743200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:53703200-53726400	Weak transcription	Fetal Stomach	stomach
3	chr6:53703800-53727600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr6:53709800-53762200	Weak transcription	Primary B cells from cord blood	blood
5	chr6:53717800-53731800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr6:53719800-53727600	Enhancers	Brain Substantia Nigra	brain
7	chr6:53719800-53727800	Enhancers	Brain Hippocampus Middle	brain
8	chr6:53719800-53747800	Weak transcription	Primary T cells from cord blood	blood
9	chr6:53720000-53727600	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr6:53720600-53741400	Weak transcription	Dnd41	blood
11	chr6:53720800-53736600	Weak transcription	Fetal Thymus	thymus
12	chr6:53721200-53726200	Weak transcription	Fetal Intestine Small	intestine
13	chr6:53721200-53726400	Weak transcription	Fetal Intestine Large	intestine
14	chr6:53721200-53726600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr6:53721200-53726800	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr6:53721600-53728000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr6:53721800-53725600	Weak transcription	Aorta	Aorta
18	chr6:53721800-53726800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr6:53722000-53748200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr6:53722400-53725400	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr6:53722600-53725400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:53722600-53725600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr6:53722600-53725600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr6:53722800-53726200	Weak transcription	HepG2	liver
25	chr6:53722800-53726400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr6:53723000-53725400	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr6:53723000-53725600	Weak transcription	Lung	lung
28	chr6:53723000-53726200	Weak transcription	HSMMtube	muscle
29	chr6:53723000-53727000	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr6:53723000-53727200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr6:53723000-53727200	Enhancers	Brain Angular Gyrus	brain
32	chr6:53723000-53728000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:53723000-53728000	Weak transcription	Pancreas	Pancrea
34	chr6:53723000-53728000	Weak transcription	Right Atrium	heart
35	chr6:53723200-53725400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr6:53723200-53725600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr6:53723200-53725600	Weak transcription	Colon Smooth Muscle	Colon
38	chr6:53723200-53725800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr6:53723400-53726000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr6:53723400-53726000	Weak transcription	HMEC	breast
41	chr6:53723400-53726000	Weak transcription	NHEK	skin
42	chr6:53723400-53726400	Weak transcription	Esophagus	oesophagus
43	chr6:53723400-53736800	Weak transcription	Stomach Mucosa	stomach
44	chr6:53724000-53726000	Weak transcription	Ovary	ovary
45	chr6:53724000-53726400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr6:53724200-53727400	Weak transcription	Thymus	Thymus
47	chr6:53724400-53725400	Weak transcription	Brain Anterior Caudate	brain
48	chr6:53724400-53725400	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr6:53724600-53725800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr6:53724800-53726600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links