Variant report

Variant	rs12754084
Chromosome Location	chr1:171737431-171737432
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:171710037..171714996-chr1:171734843..171738629,6	MCF-7	breast:
2	chr1:171734176..171737844-chr1:171748206..171752284,5	K562	blood:
3	chr1:171730299..171731843-chr1:171736543..171739308,2	K562	blood:
4	chr1:171709564..171713750-chr1:171736602..171743117,7	K562	blood:
5	chr1:171735538..171739658-chr1:171748409..171750930,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000010165	Chromatin interaction
ENSG00000236741	Chromatin interaction
ENSG00000117533	Chromatin interaction

Extended variants
information (count: 114 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10158220	0.82[EUR][1000 genomes]
rs10158235	0.83[EUR][1000 genomes]
rs10158943	0.83[EUR][1000 genomes]
rs10159080	0.83[EUR][1000 genomes]
rs10489253	0.85[CEU][hapmap];0.85[CHB][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10753190	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10753197	0.83[EUR][1000 genomes]
rs10753198	0.82[EUR][1000 genomes]
rs1079820	0.81[CEU][hapmap];0.85[CHB][hapmap];0.97[GIH][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs10798637	0.90[CHB][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10798657	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10798658	0.87[EUR][1000 genomes]
rs10798661	0.84[EUR][1000 genomes]
rs10798679	0.83[EUR][1000 genomes]
rs10913633	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913639	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10913651	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10913743	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10913799	0.83[EUR][1000 genomes]
rs10913803	0.88[CHB][hapmap];0.83[EUR][1000 genomes]
rs11579138	0.83[EUR][1000 genomes]
rs11580187	0.83[EUR][1000 genomes]
rs11585645	0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs11588649	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11589200	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11589823	0.86[EUR][1000 genomes]
rs11590059	0.88[EUR][1000 genomes]
rs11590829	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11807195	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12022693	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12022753	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12031686	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12035109	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12036580	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12063769	0.84[EUR][1000 genomes]
rs12562644	0.83[EUR][1000 genomes]
rs12723938	0.83[EUR][1000 genomes]
rs12735285	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12755791	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1555101	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1555102	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17597528	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17597542	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2206541	0.85[CEU][hapmap];0.85[CHB][hapmap];0.88[EUR][1000 genomes]
rs2206542	0.81[CEU][hapmap];0.85[CHB][hapmap];0.97[GIH][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs2232804	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2232811	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2294719	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2294720	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2294721	1.00[CEU][hapmap];0.85[CHB][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2294722	1.00[CEU][hapmap];0.85[CHB][hapmap];0.97[GIH][hapmap];0.80[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2421912	0.85[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2421913	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34219132	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35738870	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4292987	1.00[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55739261	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59592673	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6425416	1.00[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6425417	1.00[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6425422	0.96[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6425428	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6425435	0.88[EUR][1000 genomes]
rs6425436	0.88[EUR][1000 genomes]
rs6425437	0.85[CHB][hapmap];0.84[EUR][1000 genomes]
rs6425440	0.84[EUR][1000 genomes]
rs6425441	0.83[EUR][1000 genomes]
rs6656814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6657803	0.84[EUR][1000 genomes]
rs6658116	0.84[EUR][1000 genomes]
rs6658730	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6658980	0.84[EUR][1000 genomes]
rs6659621	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6665727	0.84[EUR][1000 genomes]
rs6668165	0.81[CEU][hapmap];0.85[CHB][hapmap];0.97[GIH][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs6674810	0.81[CEU][hapmap];0.84[CHB][hapmap];0.84[EUR][1000 genomes]
rs6675011	0.85[CHB][hapmap];0.84[EUR][1000 genomes]
rs6678230	0.82[EUR][1000 genomes]
rs6685030	0.90[CHB][hapmap]
rs6689108	0.84[EUR][1000 genomes]
rs6689213	0.83[EUR][1000 genomes]
rs6690544	0.85[CEU][hapmap];0.85[CHB][hapmap];0.94[GIH][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6695736	0.83[EUR][1000 genomes]
rs6698366	0.84[CHB][hapmap];0.83[EUR][1000 genomes]
rs6698467	0.83[EUR][1000 genomes]
rs6698892	0.81[CEU][hapmap];0.85[CHB][hapmap];0.83[EUR][1000 genomes]
rs6700184	0.84[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6700384	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6702424	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs732304	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs732305	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7517546	0.84[EUR][1000 genomes]
rs7517555	0.81[CEU][hapmap];0.85[CHB][hapmap];0.97[GIH][hapmap];0.86[MEX][hapmap];0.84[EUR][1000 genomes]
rs7520688	0.81[CEU][hapmap];0.85[CHB][hapmap];0.97[GIH][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs752514	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7525313	0.83[EUR][1000 genomes]
rs7537173	0.87[ASN][1000 genomes]
rs7537770	0.85[CEU][hapmap];0.85[CHB][hapmap];0.94[GIH][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7537931	0.80[EUR][1000 genomes]
rs7537935	0.80[EUR][1000 genomes]
rs7539505	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7541128	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7542691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7545100	0.83[EUR][1000 genomes]
rs7549347	0.84[EUR][1000 genomes]
rs7550603	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7552369	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7556602	0.83[CEU][hapmap];0.85[CHB][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs764179	0.83[EUR][1000 genomes]
rs764180	0.83[EUR][1000 genomes]
rs909959	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv872545	chr1:171735198-171805448	Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12754084	DCAF6	cis	cerebellum	SCAN
rs12754084	DCAF6	cis	parietal	SCAN
rs12754084	KIAA0859	Cis_1M	lymphoblastoid	RTeQTL
rs12754084	DNM3	cis	cerebellum	SCAN
rs12754084	METTL13	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171735200-171738600	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr1:171736600-171738600	Enhancers	Monocytes-CD14+_RO01746	blood
3	chr1:171737400-171738200	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr1:171737400-171738600	Enhancers	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links