Variant report

Variant	rs57317087
Chromosome Location	chr2:39992947-39992948
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39990318..39993221-chr2:40005644..40007529,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138050	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs17024157	1.00[AMR][1000 genomes]
rs17024166	1.00[AMR][1000 genomes]
rs17024174	1.00[AMR][1000 genomes]
rs17024175	1.00[AMR][1000 genomes]
rs17024189	1.00[AMR][1000 genomes]
rs17024194	1.00[AMR][1000 genomes]
rs17024197	1.00[AMR][1000 genomes]
rs17024202	1.00[AMR][1000 genomes]
rs17024206	1.00[AMR][1000 genomes]
rs17024260	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17024278	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17024282	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17024292	1.00[AMR][1000 genomes]
rs17038962	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57028848	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57564028	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58054718	1.00[AMR][1000 genomes]
rs58462460	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60131290	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72934288	1.00[AMR][1000 genomes]
rs72934295	1.00[AMR][1000 genomes]
rs72934302	1.00[AMR][1000 genomes]
rs72936018	1.00[AMR][1000 genomes]
rs72936030	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936031	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936034	1.00[AMR][1000 genomes]
rs72936037	1.00[AMR][1000 genomes]
rs72936041	1.00[AMR][1000 genomes]
rs72936044	1.00[AMR][1000 genomes]
rs72936047	1.00[AMR][1000 genomes]
rs72936048	1.00[AMR][1000 genomes]
rs72936053	1.00[AMR][1000 genomes]
rs72936058	1.00[AMR][1000 genomes]
rs72936068	1.00[AMR][1000 genomes]
rs72936072	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936073	1.00[AMR][1000 genomes]
rs72936076	1.00[AMR][1000 genomes]
rs72936078	1.00[AMR][1000 genomes]
rs72936079	1.00[AMR][1000 genomes]
rs72936085	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936089	1.00[AMR][1000 genomes]
rs72936091	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936095	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936096	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936102	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938105	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938110	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938112	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938118	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938121	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938124	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938132	0.98[AFR][1000 genomes]
rs72938134	1.00[AMR][1000 genomes]
rs72938145	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs990404	1.00[AMR][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	nsv833870	chr2:39837022-40026024	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv833881	chr2:39914558-40067256	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv873890	chr2:39976810-40009041	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv2696	chr2:39988381-40033288	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39962200-39993200	Strong transcription	Liver	Liver
2	chr2:39965200-40005000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:39965200-40005400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:39969800-39999800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr2:39971000-39999800	Weak transcription	Right Ventricle	heart
6	chr2:39971600-39998800	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr2:39972400-39998600	Strong transcription	HMEC	breast
8	chr2:39972400-39998800	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr2:39973000-39998800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr2:39974200-39998600	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr2:39974600-39994000	Strong transcription	Fetal Thymus	thymus
12	chr2:39975000-39998400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:39975000-39999800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr2:39975200-39993800	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr2:39975400-39997000	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr2:39975800-39994600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr2:39976000-39993200	Strong transcription	Placenta	Placenta
18	chr2:39976000-39993400	Strong transcription	Adipose Nuclei	Adipose
19	chr2:39976200-39995400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr2:39976200-39998800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr2:39976800-39999000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr2:39978600-40000000	Weak transcription	Fetal Heart	heart
23	chr2:39983000-39999200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr2:39983200-39994000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:39983600-39994200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr2:39983600-39996400	Strong transcription	NHDF-Ad	bronchial
27	chr2:39983600-39998600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:39983600-39999000	Strong transcription	HSMM	muscle
29	chr2:39984800-39999600	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr2:39985000-39995400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr2:39985000-39996000	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr2:39985000-40005000	Weak transcription	Colonic Mucosa	Colon
33	chr2:39985200-39996000	Weak transcription	Rectal Smooth Muscle	rectum
34	chr2:39985200-39998400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr2:39985200-39999600	Weak transcription	Brain Germinal Matrix	brain
36	chr2:39985200-39999600	Weak transcription	Psoas Muscle	Psoas
37	chr2:39985200-39999800	Weak transcription	Brain Substantia Nigra	brain
38	chr2:39985200-40005000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr2:39985400-40005200	Weak transcription	Fetal Brain Male	brain
40	chr2:39985600-40001000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr2:39985800-39995600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr2:39985800-39995800	Weak transcription	Stomach Mucosa	stomach
43	chr2:39985800-39996000	Weak transcription	Esophagus	oesophagus
44	chr2:39985800-39996000	Weak transcription	Gastric	stomach
45	chr2:39985800-39996000	Weak transcription	Pancreas	Pancrea
46	chr2:39985800-39996200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr2:39985800-39996200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr2:39985800-39996400	Weak transcription	Fetal Intestine Small	intestine
49	chr2:39985800-39999200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr2:39985800-39999400	Weak transcription	Aorta	Aorta

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