Variant report

Variant	rs9382248
Chromosome Location	chr6:53728250-53728251
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	chr6:53664494..53666032-chr6:53727700..53729812,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10755766	0.84[AMR][1000 genomes]
rs1076701	0.87[CEU][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes]
rs1076702	0.87[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes]
rs10948775	0.84[AMR][1000 genomes]
rs10948784	0.80[ASN][1000 genomes]
rs2294789	0.85[EUR][1000 genomes]
rs2294790	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2294791	0.89[EUR][1000 genomes]
rs3777661	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4236114	0.80[ASN][1000 genomes]
rs4260754	0.80[ASN][1000 genomes]
rs4314499	0.86[AMR][1000 genomes]
rs4400206	0.83[TSI][hapmap]
rs4516937	0.83[TSI][hapmap]
rs4583974	0.80[ASN][1000 genomes]
rs4624872	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs6903399	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6906921	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs6907027	0.86[CHB][hapmap]
rs6921605	0.83[TSI][hapmap]
rs7751036	0.81[CHB][hapmap]
rs7763482	0.83[TSI][hapmap]
rs9349685	0.93[CEU][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9357776	0.87[CEU][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes]
rs9370233	0.93[CEU][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9370237	0.80[ASN][1000 genomes]
rs9370241	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9382232	0.84[AMR][1000 genomes]
rs9382233	0.84[AMR][1000 genomes]
rs9382238	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9382241	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9382243	0.86[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9382244	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9382246	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9382252	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9382253	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9382254	0.93[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9382256	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9382257	0.87[AMR][1000 genomes]
rs9395876	0.84[AMR][1000 genomes]
rs9395878	0.93[CEU][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9395881	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][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:57 , 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	chr6:53709800-53762200	Weak transcription	Primary B cells from cord blood	blood
3	chr6:53717800-53731800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr6:53719800-53747800	Weak transcription	Primary T cells from cord blood	blood
5	chr6:53720600-53741400	Weak transcription	Dnd41	blood
6	chr6:53720800-53736600	Weak transcription	Fetal Thymus	thymus
7	chr6:53722000-53748200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr6:53723400-53736800	Weak transcription	Stomach Mucosa	stomach
9	chr6:53725000-53728400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr6:53725000-53729400	Enhancers	Brain Germinal Matrix	brain
11	chr6:53725400-53730000	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr6:53725400-53730200	Enhancers	Brain Anterior Caudate	brain
13	chr6:53725400-53730400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:53725600-53728600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr6:53725800-53728400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:53725800-53730000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr6:53726000-53729000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:53726000-53729000	Enhancers	HMEC	breast
19	chr6:53726200-53729600	Enhancers	Colon Smooth Muscle	Colon
20	chr6:53726400-53729000	Enhancers	Fetal Stomach	stomach
21	chr6:53726400-53730200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr6:53726600-53728400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr6:53726600-53728400	Enhancers	NH-A	brain
24	chr6:53726600-53728600	Enhancers	Muscle Satellite Cultured Cells	--
25	chr6:53726600-53729400	Enhancers	Fetal Muscle Leg	muscle
26	chr6:53726600-53730200	Enhancers	Rectal Smooth Muscle	rectum
27	chr6:53726600-53730400	Enhancers	Fetal Brain Male	brain
28	chr6:53726800-53728400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr6:53726800-53728600	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr6:53726800-53729800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr6:53727000-53728800	Weak transcription	Fetal Intestine Small	intestine
32	chr6:53727000-53729200	Enhancers	Fetal Lung	lung
33	chr6:53727200-53729000	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr6:53727200-53729400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr6:53727200-53729400	Enhancers	Fetal Brain Female	brain
36	chr6:53727400-53728400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr6:53727400-53728400	Flanking Active TSS	HSMMtube	muscle
38	chr6:53727400-53728400	Flanking Active TSS	NHEK	skin
39	chr6:53727400-53729600	Enhancers	Ovary	ovary
40	chr6:53727400-53729800	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr6:53727600-53728400	Flanking Active TSS	Brain Cingulate Gyrus	brain
42	chr6:53727600-53729000	Enhancers	Stomach Smooth Muscle	stomach
43	chr6:53727600-53730000	Enhancers	Brain Angular Gyrus	brain
44	chr6:53727600-53730400	Enhancers	Pancreatic Islets	Pancreatic Islet
45	chr6:53727600-53731200	Weak transcription	Aorta	Aorta
46	chr6:53727600-53751800	Weak transcription	Thymus	Thymus
47	chr6:53727800-53728400	Flanking Active TSS	HSMM	muscle
48	chr6:53727800-53728800	Enhancers	HepG2	liver
49	chr6:53728000-53728400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr6:53728000-53728400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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