Variant report

Variant	rs3935664
Chromosome Location	chr6:53726780-53726781
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: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10948783	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10948784	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12193567	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12194768	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12209621	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3003498	0.80[JPT][hapmap]
rs4128619	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4236114	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4260754	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4265034	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4273680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4331986	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4392712	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4486000	0.80[JPT][hapmap]
rs4583974	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4612163	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4624872	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4645423	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6458967	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6458968	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6904545	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6906921	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.95[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6907027	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6910777	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6913431	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6935621	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6935838	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7453639	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7745548	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7749635	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7749749	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7751036	1.00[CEU][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7755924	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7761285	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9296722	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9296723	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9349682	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9349683	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9349684	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9367543	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9370234	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9370237	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9370238	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9370240	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9382240	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9382242	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9382245	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9382247	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9395879	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9395880	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9395882	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9395883	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9395884	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9395887	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9463996	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs9463997	0.90[CHB][hapmap]

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:60 , 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	chr6:53703800-53727600	Weak transcription	Stomach Smooth Muscle	stomach
3	chr6:53709800-53762200	Weak transcription	Primary B cells from cord blood	blood
4	chr6:53717800-53731800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr6:53719800-53727600	Enhancers	Brain Substantia Nigra	brain
6	chr6:53719800-53727800	Enhancers	Brain Hippocampus Middle	brain
7	chr6:53719800-53747800	Weak transcription	Primary T cells from cord blood	blood
8	chr6:53720000-53727600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr6:53720600-53741400	Weak transcription	Dnd41	blood
10	chr6:53720800-53736600	Weak transcription	Fetal Thymus	thymus
11	chr6:53721200-53726800	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr6:53721600-53728000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr6:53721800-53726800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr6:53722000-53748200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr6:53723000-53727000	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr6:53723000-53727200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr6:53723000-53727200	Enhancers	Brain Angular Gyrus	brain
18	chr6:53723000-53728000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:53723000-53728000	Weak transcription	Pancreas	Pancrea
20	chr6:53723000-53728000	Weak transcription	Right Atrium	heart
21	chr6:53723400-53736800	Weak transcription	Stomach Mucosa	stomach
22	chr6:53724200-53727400	Weak transcription	Thymus	Thymus
23	chr6:53724800-53726800	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr6:53725000-53727400	Weak transcription	HUVEC	blood vessel
25	chr6:53725000-53727600	Enhancers	Brain Cingulate Gyrus	brain
26	chr6:53725000-53728400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr6:53725000-53729400	Enhancers	Brain Germinal Matrix	brain
28	chr6:53725400-53730000	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr6:53725400-53730200	Enhancers	Brain Anterior Caudate	brain
30	chr6:53725400-53730400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr6:53725600-53727000	Enhancers	Aorta	Aorta
32	chr6:53725600-53727400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr6:53725600-53728600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr6:53725800-53727400	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr6:53725800-53728400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr6:53725800-53730000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr6:53726000-53727400	Enhancers	NHEK	skin
38	chr6:53726000-53729000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr6:53726000-53729000	Enhancers	HMEC	breast
40	chr6:53726200-53727000	Enhancers	Fetal Intestine Small	intestine
41	chr6:53726200-53727400	Enhancers	HSMMtube	muscle
42	chr6:53726200-53729600	Enhancers	Colon Smooth Muscle	Colon
43	chr6:53726400-53726800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr6:53726400-53726800	Enhancers	Esophagus	oesophagus
45	chr6:53726400-53726800	Enhancers	Fetal Intestine Large	intestine
46	chr6:53726400-53726800	Enhancers	Hela-S3	cervix
47	chr6:53726400-53727400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr6:53726400-53727400	Enhancers	HSMM	muscle
49	chr6:53726400-53727600	Enhancers	NHLF	lung
50	chr6:53726400-53729000	Enhancers	Fetal Stomach	stomach

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