Variant report

Variant	rs954753
Chromosome Location	chr6:119363976-119363977
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	chr6:119363262..119365656-chr6:119366667..119368458,2	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11967399	0.82[ASN][1000 genomes]
rs11967889	0.82[ASN][1000 genomes]
rs12526935	0.99[ASN][1000 genomes]
rs1413906	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1570493	0.97[ASN][1000 genomes]
rs17513308	0.98[ASN][1000 genomes]
rs1762200	0.85[ASN][1000 genomes]
rs1775619	0.82[CHB][hapmap]
rs2051056	0.88[CHB][hapmap];0.86[CHD][hapmap]
rs2051057	0.94[CHB][hapmap]
rs2295709	0.82[CHB][hapmap];0.84[MEX][hapmap]
rs2357020	0.81[ASN][1000 genomes]
rs2357030	1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[ASN][1000 genomes]
rs2782575	0.86[ASN][1000 genomes]
rs2797352	0.84[ASN][1000 genomes]
rs284919	0.83[CEU][hapmap];0.83[CHB][hapmap]
rs2884078	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4946383	0.88[CHB][hapmap]
rs4946388	0.96[ASN][1000 genomes]
rs4946389	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4946390	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57100274	0.80[ASN][1000 genomes]
rs57285368	0.82[ASN][1000 genomes]
rs6910327	0.82[CHB][hapmap]
rs6910850	0.82[CHB][hapmap]
rs6929403	0.94[JPT][hapmap]
rs6931558	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs706978	0.82[CHB][hapmap]
rs7756475	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7764418	0.98[ASN][1000 genomes]
rs794260	0.87[ASN][1000 genomes]
rs794261	0.85[ASN][1000 genomes]
rs794262	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[ASN][1000 genomes]
rs794263	0.85[ASN][1000 genomes]
rs794264	0.85[ASN][1000 genomes]
rs794266	0.85[ASN][1000 genomes]
rs794605	0.82[EUR][1000 genomes]
rs794614	0.88[CHB][hapmap];0.83[CHD][hapmap]
rs808028	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs813812	0.87[ASN][1000 genomes]
rs9374777	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9387624	0.89[JPT][hapmap]
rs9387629	0.99[ASN][1000 genomes]
rs9387630	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9398499	0.99[ASN][1000 genomes]
rs9401113	0.82[ASN][1000 genomes]
rs9401118	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9481881	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs962393	0.82[CHB][hapmap]

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	nsv1030400	chr6:119320153-119433830	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs954753	BRD7P3	cis	parietal	SCAN
rs954753	MCM9	cis	Lymphoblastoid	GTEx
rs954753	C17orf74	trans	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119314400-119364400	Weak transcription	Fetal Muscle Trunk	muscle
2	chr6:119356400-119368800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr6:119356800-119366600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr6:119357400-119373400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr6:119359400-119364400	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr6:119360200-119364600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr6:119361200-119364400	Weak transcription	K562	blood
8	chr6:119361400-119364400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr6:119361800-119364400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr6:119362000-119364400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:119362600-119364400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr6:119362600-119364600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr6:119363400-119366600	Weak transcription	Fetal Intestine Small	intestine
14	chr6:119363600-119364600	Weak transcription	Placenta	Placenta
15	chr6:119363800-119364200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr6:119363800-119366200	Enhancers	HUES48 Cell Line	embryonic stem cell

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