Variant report

Variant	rs12141134
Chromosome Location	chr1:179918897-179918898
allele	A/G
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	JUND	chr1:179918877-179919096	HepG2	liver:	n/a	chr1:179919001-179919010
2	JUN	chr1:179918860-179919080	HepG2	liver:	n/a	chr1:179919000-179919013 chr1:179919001-179919010

No.	Distal block	Cell Line	Cell type
1	chr1:179908000..179910722-chr1:179917793..179921003,3	MCF-7	breast:
2	chr1:179908035..179914745-chr1:179916684..179919859,6	K562	blood:
3	chr1:179785178..179788350-chr1:179915733..179919053,3	K562	blood:
4	chr1:179918538..179920784-chr1:179921787..179924203,3	MCF-7	breast:
5	chr1:179917458..179921569-chr1:179921680..179924847,7	K562	blood:
6	chr1:179907154..179913357-chr1:179915865..179919035,6	K562	blood:
7	chr1:179916956..179919742-chr1:179919883..179921705,2	MCF-7	breast:

Variant related genes	Relation type
CEP350	TF binding region
ENSG00000135837	Chromatin interaction
ENSG00000260360	Chromatin interaction
ENSG00000229407	Chromatin interaction
ENSG00000261831	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1048418	1.00[CHD][hapmap]
rs10913920	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12116940	1.00[ASN][1000 genomes]
rs12118265	1.00[ASN][1000 genomes]
rs12119130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12121845	0.80[TSI][hapmap]
rs12123560	0.80[TSI][hapmap]
rs12125245	0.89[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];1.00[ASN][1000 genomes]
rs12125592	1.00[ASN][1000 genomes]
rs12126496	1.00[ASN][1000 genomes]
rs12126967	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];1.00[ASN][1000 genomes]
rs12127784	1.00[ASN][1000 genomes]
rs12129115	1.00[ASN][1000 genomes]
rs12130673	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12130720	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12131200	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12132694	0.80[TSI][hapmap]
rs12133136	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12136091	1.00[CHB][hapmap]
rs12138429	1.00[ASN][1000 genomes]
rs12139040	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12139323	0.80[TSI][hapmap]
rs12140622	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12142457	1.00[CHB][hapmap]
rs12144328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12144346	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];1.00[ASN][1000 genomes]
rs12144352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];1.00[ASN][1000 genomes]
rs12144853	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12184265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs16855021	0.80[TSI][hapmap]
rs16855022	0.80[TSI][hapmap]
rs16855025	0.80[TSI][hapmap]
rs16855048	0.80[TSI][hapmap]
rs16855107	0.80[TSI][hapmap]
rs16855110	0.80[TSI][hapmap]
rs16855125	0.80[CEU][hapmap]
rs16855130	0.80[TSI][hapmap]
rs17299006	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17371159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17371267	1.00[ASN][1000 genomes]
rs17371308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];1.00[ASN][1000 genomes]
rs1801795	1.00[ASN][1000 genomes]
rs3845388	1.00[CHD][hapmap]
rs3856049	1.00[ASN][1000 genomes]
rs4301600	1.00[CHD][hapmap]
rs9701232	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9701237	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv429947	chr1:179790518-179925104	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12141134	CEP350	Cis_1M	lymphoblastoid	RTeQTL
rs12141134	RALGPS2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179918600-179919400	Enhancers	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links