Variant report

Variant	rs12741128
Chromosome Location	chr1:95568038-95568039
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:95567873..95570804-chr1:95585037..95586661,2	K562	blood:
2	chr1:95566799..95569108-chr1:95574086..95576514,2	K562	blood:
3	chr1:95566404..95569309-chr1:95582232..95584413,3	K562	blood:
4	chr1:95538014..95540644-chr1:95567709..95569677,2	K562	blood:
5	chr1:95561720..95565038-chr1:95567482..95569878,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231992	Chromatin interaction
ENSG00000172339	Chromatin interaction
ENSG00000271092	Chromatin interaction
ENSG00000152078	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1023330	0.84[CHB][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10493880	0.91[ASW][hapmap];0.96[CEU][hapmap];0.87[GIH][hapmap];0.95[TSI][hapmap]
rs10735790	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10782996	0.85[ASN][1000 genomes]
rs10874902	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11165299	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11585462	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11591183	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12563424	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12563592	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12569038	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12569207	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1265169	0.83[ASW][hapmap];0.83[TSI][hapmap]
rs12748237	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12751774	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2391388	0.92[CHB][hapmap];0.96[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs2391389	0.84[ASN][1000 genomes]
rs2766010	0.91[ASW][hapmap];0.96[CEU][hapmap];0.84[CHB][hapmap];0.98[GIH][hapmap];0.97[TSI][hapmap]
rs34280926	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35678413	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35888232	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4245670	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4259714	0.82[ASN][1000 genomes]
rs4309032	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4339907	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4344373	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4390223	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4630159	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.91[LWK][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4847220	0.96[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap];0.80[EUR][1000 genomes]
rs4949965	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.81[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4950056	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4950057	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4950058	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.91[LWK][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4950077	0.92[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4950083	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6675668	1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs6683112	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6687388	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6687450	1.00[CEU][hapmap];0.89[CHB][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6698046	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.97[TSI][hapmap]
rs7533303	0.84[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap]
rs7537374	0.92[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs7539139	0.84[ASN][1000 genomes]
rs7547662	0.84[CHB][hapmap]
rs9437665	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9437672	0.94[ASN][1000 genomes]
rs9437689	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9437810	0.94[ASN][1000 genomes]
rs9437812	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9437813	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9661031	0.83[EUR][1000 genomes];0.88[ASN][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	nsv830636	chr1:95495849-95703126	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12741128	ABCD3	cis	cerebellum	SCAN
rs12741128	PTBP2	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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