Variant report

Variant	rs12138072
Chromosome Location	chr1:47788979-47788980
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:47780261..47782876-chr1:47787046..47789299,3	MCF-7	breast:
2	chr1:47695594..47698259-chr1:47788748..47790868,3	K562	blood:
3	chr1:47777717..47780108-chr1:47788824..47790541,2	K562	blood:
4	chr1:47748082..47750249-chr1:47787752..47790468,2	K562	blood:
5	chr1:47788958..47792028-chr1:47798219..47801724,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123473	Chromatin interaction
ENSG00000162368	Chromatin interaction
ENSG00000162367	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10157883	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1028646	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1028647	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1044457	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11211510	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11211511	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11211517	0.91[ASW][hapmap];1.00[CEU][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12118514	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12119783	0.82[ASN][1000 genomes]
rs12121831	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12125261	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12126139	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12127982	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12132928	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12141060	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12562561	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12730819	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12731806	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12732050	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12732410	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12743643	0.95[ASN][1000 genomes]
rs12743877	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17370337	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17452995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2246707	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2472725	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2494247	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2622901	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2622905	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2622907	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2622908	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2622925	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2622926	0.87[ASN][1000 genomes]
rs2742081	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2742104	0.96[CEU][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2758735	0.96[CEU][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2758737	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2820987	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2820988	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2820989	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2821087	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2821088	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2821090	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2821093	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2821094	0.81[AMR][1000 genomes]
rs2821096	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3122607	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3122610	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3122611	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3122615	0.96[CEU][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3122619	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3122620	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3122623	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3125624	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3125628	0.91[ASW][hapmap];0.96[CEU][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3125630	0.96[CEU][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3125632	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3125633	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3125638	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3125639	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3125640	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3125641	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34400183	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34952704	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35711761	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35774681	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35880845	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3814003	0.94[JPT][hapmap]
rs3925058	0.96[CEU][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4147192	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4492666	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4926824	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55737131	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56270164	0.82[ASN][1000 genomes]
rs56328227	0.82[ASN][1000 genomes]
rs61782706	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6588348	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6588365	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6659946	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6671254	0.96[CEU][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6681868	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6689687	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6692734	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6703956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6795	0.89[CEU][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71645861	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72686249	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7523987	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7525650	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7533562	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7541748	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7543016	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9436749	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9436838	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9436882	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][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	esv3390574	chr1:47778981-47803091	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12138072	CMPK	Cis_1M	lymphoblastoid	RTeQTL
rs12138072	CMPK1	cis	parietal	SCAN
rs12138072	CMPK1	cis	lymphoblastoid	seeQTL
rs12138072	MKNK1	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47780200-47798400	Weak transcription	Spleen	Spleen
2	chr1:47780600-47798000	Weak transcription	HSMMtube	muscle
3	chr1:47780800-47789200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:47780800-47791200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:47780800-47797800	Weak transcription	Fetal Muscle Leg	muscle
6	chr1:47787200-47790800	Enhancers	Stomach Mucosa	stomach
7	chr1:47787800-47789600	Enhancers	HepG2	liver
8	chr1:47788200-47791800	Enhancers	Fetal Intestine Small	intestine
9	chr1:47788400-47789200	Weak transcription	Duodenum Mucosa	Duodenum
10	chr1:47788600-47792400	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr1:47788800-47789800	Enhancers	K562	blood
12	chr1:47788800-47790200	Enhancers	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links