Variant report

Variant	rs2178474
Chromosome Location	chr2:173375472-173375473
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10174809	0.87[CHB][hapmap];0.81[ASN][1000 genomes]
rs10175670	0.85[JPT][hapmap]
rs10195932	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs10197251	0.82[JPT][hapmap]
rs10205409	0.99[AFR][1000 genomes]
rs10208469	0.96[AFR][1000 genomes]
rs10497381	0.82[JPT][hapmap]
rs10497385	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs1076595	0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10803874	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs12465295	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12465442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12467358	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12469875	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs12469958	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12474168	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12474995	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12475916	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12476126	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12477247	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12477594	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12478465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12619242	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12622687	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13383151	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13402061	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1344272	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs1574247	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16860377	0.82[JPT][hapmap]
rs16860543	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16860805	1.00[CEU][hapmap]
rs16860809	1.00[CEU][hapmap]
rs2084732	1.00[CEU][hapmap]
rs2178477	0.96[AFR][1000 genomes]
rs2293646	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293649	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2357415	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34094408	0.94[ASN][1000 genomes]
rs3749148	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs3762619	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs3792257	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3792260	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3934627	0.85[JPT][hapmap]
rs4281870	0.80[EUR][1000 genomes]
rs4308101	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4480959	0.82[JPT][hapmap]
rs4619573	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs4972515	1.00[CEU][hapmap]
rs4972839	0.86[ASN][1000 genomes]
rs4972851	1.00[CEU][hapmap]
rs56084828	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57418091	0.84[EUR][1000 genomes]
rs57957394	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58016698	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58044442	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59020762	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59524026	0.85[ASN][1000 genomes]
rs59610589	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60275829	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60442917	0.85[ASN][1000 genomes]
rs60446415	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61542159	0.86[EUR][1000 genomes]
rs6718477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6727229	0.96[AFR][1000 genomes]
rs6755100	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72894386	0.86[ASN][1000 genomes]
rs733331	1.00[CEU][hapmap]
rs7564591	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs7564654	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs7565216	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7582972	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs7589362	0.84[AFR][1000 genomes]
rs7591883	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7609465	0.82[ASN][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:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173347800-173376200	Weak transcription	Fetal Heart	heart
2	chr2:173356400-173379200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:173356800-173376000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr2:173356800-173376200	Weak transcription	Brain Substantia Nigra	brain
5	chr2:173357000-173376000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr2:173357000-173376000	Weak transcription	Aorta	Aorta
7	chr2:173357200-173376600	Weak transcription	Right Ventricle	heart
8	chr2:173357600-173376200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:173358000-173376200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr2:173361000-173375600	Weak transcription	Spleen	Spleen
11	chr2:173367400-173376000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr2:173369600-173375600	Weak transcription	Liver	Liver
13	chr2:173369600-173376000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr2:173369600-173376000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr2:173369600-173376000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr2:173369600-173376000	Weak transcription	Esophagus	oesophagus
17	chr2:173369600-173376000	Weak transcription	HUVEC	blood vessel
18	chr2:173369800-173375600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr2:173369800-173375600	Weak transcription	Adipose Nuclei	Adipose
20	chr2:173369800-173376600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr2:173370200-173375600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr2:173370400-173375600	Weak transcription	Brain Anterior Caudate	brain
23	chr2:173371400-173375800	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr2:173372200-173375600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr2:173372400-173377000	Weak transcription	Thymus	Thymus
26	chr2:173372600-173379600	Enhancers	Primary B cells from peripheral blood	blood
27	chr2:173373200-173375800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr2:173373200-173376200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr2:173373200-173376200	Weak transcription	NHEK	skin
30	chr2:173373200-173376400	Weak transcription	Fetal Thymus	thymus
31	chr2:173373400-173375800	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr2:173373400-173375800	Weak transcription	Pancreas	Pancrea
33	chr2:173373400-173376000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr2:173373400-173376000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr2:173373400-173376400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr2:173373600-173376400	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr2:173373800-173375600	Weak transcription	HMEC	breast
38	chr2:173373800-173376000	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr2:173374200-173376000	Enhancers	Primary hematopoietic stem cells	blood
40	chr2:173374200-173376000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr2:173374200-173376400	Enhancers	Primary T cells fromperipheralblood	blood
42	chr2:173374200-173376600	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr2:173374400-173375600	Weak transcription	HSMM	muscle
44	chr2:173374400-173375800	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr2:173374600-173375800	Flanking Active TSS	Primary B cells from cord blood	blood
46	chr2:173374800-173375600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
47	chr2:173374800-173375800	Flanking Active TSS	Primary T cells from cord blood	blood
48	chr2:173374800-173376000	Enhancers	Primary neutrophils fromperipheralblood	blood
49	chr2:173374800-173376600	Strong transcription	HSMMtube	muscle
50	chr2:173375000-173375600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood

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