Variant report

Variant	rs661015
Chromosome Location	chr2:31498040-31498041
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	chr2:31495749..31498208-chr2:31503844..31506065,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1010477	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10175943	0.91[ASN][1000 genomes]
rs11124256	0.91[ASN][1000 genomes]
rs11683836	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12988379	1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1474941	0.91[ASN][1000 genomes]
rs2145036	0.91[ASN][1000 genomes]
rs4366947	0.87[ASN][1000 genomes]
rs4951976	0.86[ASN][1000 genomes]
rs4951977	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4952077	0.91[ASN][1000 genomes]
rs4952078	0.86[ASN][1000 genomes]
rs585805	0.82[EUR][1000 genomes]
rs586245	0.86[ASN][1000 genomes]
rs590009	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs598204	0.82[ASN][1000 genomes]
rs600236	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs602322	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs602771	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs603824	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs604127	1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs604986	0.89[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]
rs631396	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs635092	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs637911	0.91[ASN][1000 genomes]
rs644417	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs644736	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs646103	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs646200	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6543622	0.91[ASN][1000 genomes]
rs674791	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs684967	0.82[ASN][1000 genomes]
rs7567147	0.86[ASN][1000 genomes]
rs7581173	0.86[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	nsv948552	chr2:31118599-31595424	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs661015	IFT172	cis	parietal	SCAN
rs661015	UCN	cis	cerebellum	SCAN
rs661015	EHD3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:31459400-31498600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr2:31463600-31501400	Weak transcription	Pancreas	Pancrea
3	chr2:31468200-31501600	Weak transcription	Primary hematopoietic stem cells	blood
4	chr2:31482000-31501000	Weak transcription	Fetal Intestine Large	intestine
5	chr2:31482600-31501400	Weak transcription	Liver	Liver
6	chr2:31486600-31510000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:31490000-31502400	Weak transcription	Spleen	Spleen
8	chr2:31490600-31498600	Weak transcription	Brain Germinal Matrix	brain
9	chr2:31491400-31498600	Enhancers	Placenta	Placenta
10	chr2:31491400-31499800	Weak transcription	Fetal Brain Female	brain
11	chr2:31492400-31507800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr2:31492800-31510600	Weak transcription	Aorta	Aorta
13	chr2:31494400-31498600	Weak transcription	Fetal Kidney	kidney
14	chr2:31494400-31505600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr2:31494800-31498400	Enhancers	Fetal Stomach	stomach
16	chr2:31495600-31499200	Enhancers	Fetal Lung	lung
17	chr2:31495800-31509800	Weak transcription	Esophagus	oesophagus
18	chr2:31497000-31501600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr2:31497000-31510400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr2:31497200-31502600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr2:31497400-31498800	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr2:31497400-31501000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr2:31497600-31499600	Enhancers	Right Ventricle	heart
24	chr2:31497800-31498200	Enhancers	Fetal Muscle Trunk	muscle
25	chr2:31498000-31498200	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:31498000-31498200	Enhancers	Ovary	ovary
27	chr2:31498000-31499600	Enhancers	Left Ventricle	heart
28	chr2:31498000-31500000	Enhancers	Fetal Heart	heart

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