Variant report

Variant	rs13179975
Chromosome Location	chr5:154477010-154477011
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	chr5:154475458..154478110-chr5:154501032..154502578,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10071858	1.00[ASN][1000 genomes]
rs10078853	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1025301	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10454998	0.83[AFR][1000 genomes]
rs11167710	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs12153388	0.80[AFR][1000 genomes]
rs12187203	0.83[AFR][1000 genomes]
rs12187264	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13154769	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13159706	0.80[AFR][1000 genomes]
rs13165083	0.80[AFR][1000 genomes]
rs13167540	0.83[AFR][1000 genomes]
rs17650275	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34974326	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36059089	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958397	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs4958778	0.80[AFR][1000 genomes]
rs4958781	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs4958782	0.80[AFR][1000 genomes]
rs6580134	0.88[EUR][1000 genomes]
rs66691937	1.00[ASN][1000 genomes]
rs67562605	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6859744	0.85[EUR][1000 genomes]
rs6869991	1.00[ASN][1000 genomes]
rs6870353	0.80[EUR][1000 genomes]
rs7713042	1.00[ASN][1000 genomes]
rs7715693	0.91[CEU][hapmap];1.00[YRI][hapmap]
rs7719709	0.91[CEU][hapmap];1.00[YRI][hapmap]
rs7722477	0.88[EUR][1000 genomes]
rs7724975	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7733613	0.88[EUR][1000 genomes]
rs7733811	0.85[EUR][1000 genomes]
rs7736559	0.86[EUR][1000 genomes];1.00[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	nsv883059	chr5:154457905-154556230	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13179975	SGCD	cis	parietal	SCAN
rs13179975	ITK	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154472400-154483000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:154472800-154477600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr5:154475000-154477600	Weak transcription	Left Ventricle	heart
4	chr5:154476000-154477800	Weak transcription	Fetal Heart	heart
5	chr5:154476000-154477800	Weak transcription	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links