Variant report

Variant	rs12197688
Chromosome Location	chr6:131146285-131146286
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr6:131146051-131146532	HepG2	liver:	n/a	n/a
2	TEAD4	chr6:131145994-131146596	HepG2	liver:	n/a	n/a
3	FOXA1	chr6:131145995-131146557	HepG2	liver:	n/a	n/a
4	FOXA1	chr6:131146018-131146526	HepG2	liver:	n/a	n/a
5	FOXA2	chr6:131145979-131146411	HepG2	liver:	n/a	n/a
6	ARID3A	chr6:131145980-131146464	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
SMLR1	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1008688	0.84[CEU][hapmap]
rs10457561	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10457562	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10457563	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12176542	1.00[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12208586	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3777432	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6942054	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71551706	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9375773	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9375778	1.00[JPT][hapmap]
rs9385567	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9388853	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9388854	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9388860	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9398963	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9398964	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9402283	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9402293	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9402295	1.00[JPT][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	nsv533971	chr6:130490694-131172051	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12197688	EPB41L2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131132000-131159200	Weak transcription	HSMM	muscle
2	chr6:131132000-131173800	Weak transcription	HSMMtube	muscle
3	chr6:131136400-131174400	Weak transcription	Left Ventricle	heart
4	chr6:131138400-131147400	Weak transcription	Fetal Intestine Large	intestine
5	chr6:131142600-131147600	Enhancers	HepG2	liver
6	chr6:131143600-131146400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:131145600-131148400	Weak transcription	Psoas Muscle	Psoas
8	chr6:131145800-131146400	Enhancers	Duodenum Mucosa	Duodenum
9	chr6:131145800-131147800	Enhancers	Liver	Liver
10	chr6:131145800-131148000	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr6:131146000-131147200	Weak transcription	Fetal Intestine Small	intestine
12	chr6:131146200-131147000	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr6:131146200-131148000	Enhancers	ES-I3 Cell Line	embryonic stem cell

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