Variant report

Variant	rs10494442
Chromosome Location	chr1:165255228-165255229
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:165253102..165255836-chr1:165256006..165257807,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10918144	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs10918145	1.00[CHB][hapmap];0.91[CHD][hapmap];0.85[ASN][1000 genomes]
rs12135437	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.81[MEX][hapmap];0.81[EUR][1000 genomes]
rs12404307	1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs12405561	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12411054	0.85[ASN][1000 genomes]
rs1343554	0.85[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs16841924	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[MEX][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs17404691	1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs1811714	1.00[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap];0.81[EUR][1000 genomes]
rs34458079	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4361970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.92[JPT][hapmap];0.93[MEX][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55743629	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56274812	0.85[ASN][1000 genomes]
rs56820548	0.87[ASN][1000 genomes]
rs59974691	0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6677100	0.91[ASN][1000 genomes]
rs7518895	0.88[ASN][1000 genomes]
rs7519089	1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[ASN][1000 genomes]
rs7528111	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.96[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	nsv869712	chr1:164866810-165299085	Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10494442	KCNJ10	cis	cerebellum	SCAN
rs10494442	CD247	cis	cerebellum	SCAN
rs10494442	FCRLA	cis	cerebellum	SCAN
rs10494442	NR1I3	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165248800-165256600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:165251600-165256600	Weak transcription	HepG2	liver
3	chr1:165253600-165258200	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr1:165254600-165258800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr1:165254800-165257200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:165254800-165258800	Enhancers	Liver	Liver

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