Variant report

Variant	rs12052385
Chromosome Location	chr2:173316217-173316218
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	chr2:173314991..173316624-chr2:173316906..173318533,2	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1001926	1.00[AFR][1000 genomes]
rs10187564	1.00[EUR][1000 genomes]
rs10207640	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10207654	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10210544	0.85[JPT][hapmap]
rs10930559	1.00[CEU][hapmap];0.83[GIH][hapmap];0.85[EUR][1000 genomes]
rs12052253	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[EUR][1000 genomes]
rs12053442	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12613307	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12615584	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12615596	0.96[EUR][1000 genomes]
rs12621278	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12622724	1.00[CEU][hapmap];0.80[CHD][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs13410475	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[EUR][1000 genomes]
rs13414928	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1574256	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1574259	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16860397	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16860416	0.84[JPT][hapmap]
rs16860419	0.87[CHB][hapmap];0.92[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16860426	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs16860438	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs16860478	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs16860513	1.00[CEU][hapmap]
rs16860515	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs16860634	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs2008518	1.00[AFR][1000 genomes]
rs2178476	1.00[AFR][1000 genomes]
rs2272496	1.00[AFR][1000 genomes]
rs2293645	1.00[CEU][hapmap];0.83[GIH][hapmap];0.85[EUR][1000 genomes]
rs2293647	1.00[CEU][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2293648	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs28485589	0.90[EUR][1000 genomes]
rs3762618	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[EUR][1000 genomes]
rs4405725	1.00[CEU][hapmap];0.85[JPT][hapmap];0.96[EUR][1000 genomes]
rs55867175	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs56882727	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs56892098	0.90[EUR][1000 genomes]
rs57244773	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs57404607	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs57587465	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs57878744	0.90[EUR][1000 genomes]
rs59374567	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs59454075	1.00[EUR][1000 genomes]
rs59970483	0.85[EUR][1000 genomes]
rs60096331	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6730284	0.85[EUR][1000 genomes]
rs6741759	0.85[EUR][1000 genomes]
rs9636257	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173305000-173316800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr2:173306800-173316400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:173307200-173318600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:173307400-173322400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr2:173307600-173321000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr2:173309000-173317000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:173310400-173318000	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr2:173310800-173317000	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr2:173310800-173318200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr2:173310800-173318600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr2:173310800-173319800	Weak transcription	Fetal Muscle Leg	muscle
12	chr2:173310800-173320000	Weak transcription	Lung	lung
13	chr2:173310800-173322400	Weak transcription	Thymus	Thymus
14	chr2:173311000-173316400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr2:173311400-173318000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr2:173311600-173316400	Weak transcription	Adipose Nuclei	Adipose
17	chr2:173311600-173317200	Weak transcription	Liver	Liver
18	chr2:173311600-173319000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr2:173311600-173319200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr2:173311600-173319200	Weak transcription	HUVEC	blood vessel
21	chr2:173311800-173317200	Weak transcription	Fetal Thymus	thymus
22	chr2:173311800-173319200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr2:173312200-173317000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr2:173312200-173319400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr2:173312200-173323600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr2:173312400-173319200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr2:173312600-173316400	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr2:173313200-173319800	Weak transcription	Fetal Kidney	kidney
29	chr2:173313400-173317000	Weak transcription	Fetal Lung	lung
30	chr2:173313600-173323400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr2:173313800-173316800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:173313800-173319200	Weak transcription	HepG2	liver
33	chr2:173314000-173316400	Weak transcription	Left Ventricle	heart
34	chr2:173314000-173316400	Weak transcription	Pancreas	Pancrea
35	chr2:173314000-173318600	Weak transcription	Colonic Mucosa	Colon
36	chr2:173314200-173319200	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr2:173314200-173319200	Weak transcription	Hela-S3	cervix
38	chr2:173314400-173317200	Weak transcription	Right Ventricle	heart
39	chr2:173314400-173317400	Weak transcription	Fetal Intestine Large	intestine
40	chr2:173314400-173318600	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr2:173314400-173319400	Weak transcription	Fetal Intestine Small	intestine
42	chr2:173314600-173316800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr2:173314800-173319000	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr2:173315000-173316400	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr2:173315000-173316400	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr2:173315000-173316400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr2:173315000-173316400	Weak transcription	Right Atrium	heart
48	chr2:173315000-173317800	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr2:173315000-173320000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr2:173315000-173320800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links