Variant report

Variant	rs12192603
Chromosome Location	chr6:24342371-24342372
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:24341482..24343826-chr6:24359222..24360846,2	MCF-7	breast:
2	chr6:24341614..24344707-chr6:24345325..24348504,3	MCF-7	breast:
3	chr6:24339050..24344227-chr6:24347020..24349931,5	MCF-7	breast:
4	chr6:24338936..24342390-chr6:24350898..24353843,3	MCF-7	breast:
5	chr6:24340134..24343269-chr6:24348514..24352207,3	MCF-7	breast:
6	chr6:24333030..24335051-chr6:24339193..24343115,3	MCF-7	breast:
7	chr6:24341268..24343493-chr6:24355981..24357626,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000146049	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs12189743	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12192494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1923168	0.95[ASN][1000 genomes]
rs1923169	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2185597	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2328819	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4412188	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4445044	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4496795	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4541735	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4580860	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4599626	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456605	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456608	0.86[JPT][hapmap]
rs6904234	1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs6940827	0.85[JPT][hapmap]
rs7751169	0.86[JPT][hapmap]
rs7754567	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7759923	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7770684	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7775064	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7775357	0.86[JPT][hapmap]
rs793649	0.86[JPT][hapmap]
rs793650	0.86[JPT][hapmap]
rs793659	0.86[JPT][hapmap]
rs793698	0.86[JPT][hapmap]
rs793720	0.86[JPT][hapmap]
rs793721	0.84[JPT][hapmap]
rs793722	0.85[JPT][hapmap]
rs9460992	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9460994	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467117	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467121	0.86[JPT][hapmap]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12192603	NKAPL	cis	parietal	SCAN
rs12192603	HFE	cis	parietal	SCAN
rs12192603	HIST1H2BO	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24339600-24355600	Weak transcription	Pancreas	Pancrea
2	chr6:24341000-24342600	Enhancers	Liver	Liver
3	chr6:24341200-24342600	Enhancers	Fetal Kidney	kidney
4	chr6:24341200-24357600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:24341400-24346200	Weak transcription	Fetal Intestine Small	intestine
6	chr6:24341800-24342600	Flanking Active TSS	HepG2	liver
7	chr6:24342000-24342400	Enhancers	Fetal Lung	lung
8	chr6:24342000-24342600	Flanking Active TSS	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links