Variant report

Variant	rs11174122
Chromosome Location	chr12:62048870-62048871
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:62048195..62048935-chr12:62399595..62401023,3	MCF-7	breast:
2	chr12:62048211..62049119-chr12:62586208..62587064,4	MCF-7	breast:
3	chr12:62048165..62049231-chr12:62387283..62388132,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198673	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10877700	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10877707	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877713	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10877714	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10877715	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10877717	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10877719	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10877723	0.82[YRI][hapmap]
rs10877724	0.85[YRI][hapmap]
rs10877727	0.85[YRI][hapmap]
rs11174116	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11174125	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174126	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174141	0.81[ASW][hapmap];0.85[YRI][hapmap]
rs11609247	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11834964	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12369048	0.84[YRI][hapmap]
rs12422748	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12579881	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12582016	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1395490	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1580975	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2063063	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34032839	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4616113	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61941851	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7958577	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7974797	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042044	chr12:61256015-62196885	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1039741	chr12:62046850-62491052	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11174122	RPL41	cis	cerebellum	SCAN
rs11174122	R3HDM2	cis	cerebellum	SCAN
rs11174122	OS9	cis	cerebellum	SCAN
rs11174122	SCN4A	trans	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:62047800-62049000	Enhancers	HUES6 Cell Line	embryonic stem cell
2	chr12:62047800-62049200	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr12:62047800-62049400	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr12:62047800-62049400	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr12:62048200-62049200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
6	chr12:62048200-62049400	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr12:62048600-62049000	Enhancers	H1 Cell Line	embryonic stem cell
8	chr12:62048600-62049000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr12:62048600-62049000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr12:62048600-62049000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:62048600-62049000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:62048600-62049800	Enhancers	H9 Cell Line	embryonic stem cell
13	chr12:62048800-62049200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell

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