Variant report

Variant	rs4950023
Chromosome Location	chr1:97658395-97658396
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	chr1:97658017..97658973-chr1:97991101..97992019,3	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10430074	1.00[CHD][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875054	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875055	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[ASN][1000 genomes]
rs12127420	0.95[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133667	1.00[CHB][hapmap]
rs1413227	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap]
rs1413229	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1413231	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1413235	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs17471125	1.00[CHB][hapmap]
rs1970142	1.00[ASN][1000 genomes]
rs28619552	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762412	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4128472	0.81[YRI][hapmap]
rs494271	1.00[CHB][hapmap]
rs4949945	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs496179	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs533365	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap]
rs595937	1.00[ASN][1000 genomes]
rs6593632	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6593635	1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6593636	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6593637	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6593639	0.85[YRI][hapmap]
rs6661442	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6673282	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6681752	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6683351	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6683883	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6692424	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6693034	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6697132	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs6700957	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67665424	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs688913	1.00[ASN][1000 genomes]
rs7513333	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7528359	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7531100	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7537668	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs7545506	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs828052	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[ASN][1000 genomes]
rs828054	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[ASN][1000 genomes]
rs828058	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs885622	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs914959	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[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	nsv491816	chr1:97266403-98223619	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv530048	chr1:97457175-98031501	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1007950	chr1:97466488-98021146	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:97620200-97658400	Weak transcription	Lung	lung
2	chr1:97626600-97660400	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr1:97635400-97658400	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr1:97636000-97660400	Weak transcription	Right Ventricle	heart
5	chr1:97639600-97658400	Weak transcription	HSMM	muscle
6	chr1:97640000-97663000	Weak transcription	Esophagus	oesophagus
7	chr1:97641200-97658400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr1:97643600-97660200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr1:97645400-97660200	Weak transcription	Left Ventricle	heart
10	chr1:97648800-97659800	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr1:97649000-97659800	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr1:97649000-97661200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr1:97649600-97662400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr1:97651800-97669800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr1:97652800-97658800	Strong transcription	Primary B cells from cord blood	blood
16	chr1:97653400-97660800	Weak transcription	Ovary	ovary
17	chr1:97653600-97659000	Strong transcription	Liver	Liver
18	chr1:97654000-97660200	Strong transcription	Primary T cells from cord blood	blood
19	chr1:97654200-97671200	Weak transcription	Small Intestine	intestine
20	chr1:97654600-97659400	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr1:97655800-97658600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr1:97655800-97659200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr1:97656000-97659400	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr1:97656000-97659400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:97656200-97658400	Weak transcription	Colon Smooth Muscle	Colon
26	chr1:97656200-97658400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr1:97656200-97668000	Weak transcription	Brain Cingulate Gyrus	brain
28	chr1:97656400-97658600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr1:97656600-97658400	Weak transcription	Brain Substantia Nigra	brain
30	chr1:97656600-97658800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr1:97656600-97664400	Weak transcription	Fetal Brain Male	brain
32	chr1:97656800-97659600	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr1:97657000-97659400	Strong transcription	Dnd41	blood
34	chr1:97657000-97660000	Weak transcription	Duodenum Mucosa	Duodenum
35	chr1:97657200-97658800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr1:97657200-97658800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:97657200-97659200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr1:97657200-97659400	Weak transcription	Fetal Thymus	thymus
39	chr1:97657200-97671200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr1:97657400-97658600	Enhancers	Brain Germinal Matrix	brain
41	chr1:97657400-97659800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr1:97657400-97659800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr1:97657400-97664800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr1:97657600-97658800	Strong transcription	Adipose Nuclei	Adipose
45	chr1:97657800-97658400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr1:97657800-97659200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr1:97657800-97659200	Enhancers	Muscle Satellite Cultured Cells	--
48	chr1:97657800-97659400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr1:97658000-97658400	Enhancers	NHEK	skin
50	chr1:97658000-97658600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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