Variant report

Variant	rs1369846
Chromosome Location	chr1:224894095-224894096
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	chr1:224890636..224894116-chr1:224907021..224910162,3	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10799277	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs10915694	0.82[CEU][hapmap];0.80[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10915696	0.80[EUR][1000 genomes]
rs10915698	0.80[CEU][hapmap];0.84[EUR][1000 genomes]
rs10915699	0.82[ASW][hapmap];0.80[CEU][hapmap];0.80[MEX][hapmap];0.86[EUR][1000 genomes]
rs12092438	0.81[EUR][1000 genomes]
rs13374487	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1369847	0.80[EUR][1000 genomes]
rs1436171	0.82[ASW][hapmap];0.80[CEU][hapmap];0.84[EUR][1000 genomes]
rs1465768	0.82[ASW][hapmap];0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs1561110	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1965776	0.94[ASW][hapmap];0.95[CEU][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1965777	0.86[EUR][1000 genomes]
rs2405525	0.86[EUR][1000 genomes]
rs2897161	0.85[EUR][1000 genomes]
rs4147293	0.80[EUR][1000 genomes]
rs4653591	0.80[EUR][1000 genomes]
rs56881651	0.87[EUR][1000 genomes]
rs61676104	0.87[EUR][1000 genomes]
rs6686604	0.81[EUR][1000 genomes]
rs6686633	0.81[EUR][1000 genomes]
rs7511897	0.84[CEU][hapmap];0.89[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7542431	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7542995	0.82[CEU][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs873594	0.82[ASW][hapmap];0.80[CEU][hapmap];0.84[EUR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1369846	RAB3GAP2	cis	cerebellum	SCAN
rs1369846	DEGS1	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224862400-224902000	Weak transcription	Pancreas	Pancrea
2	chr1:224881400-224895400	Weak transcription	Ovary	ovary
3	chr1:224885000-224920200	Weak transcription	Right Atrium	heart
4	chr1:224885600-224895200	Weak transcription	NH-A	brain
5	chr1:224885800-224895200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:224888400-224894200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:224888800-224895600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:224889800-224895600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:224892000-224895600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:224892000-224895600	Weak transcription	NHLF	lung
11	chr1:224892400-224895600	Weak transcription	Dnd41	blood
12	chr1:224893000-224895400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:224893200-224895400	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr1:224893200-224895600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:224893400-224894400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr1:224893800-224894200	Enhancers	H9 Cell Line	embryonic stem cell
17	chr1:224894000-224894200	Enhancers	NHDF-Ad	bronchial

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