Variant report

Variant	rs3742959
Chromosome Location	chr15:58249113-58249114
allele	C/T
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	POLR2A	chr15:58248994-58249266	K562	blood:	n/a	n/a
2	POLR2A	chr15:58248742-58249819	K562	blood:	n/a	n/a
3	POLR2A	chr15:58242506-58254000	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:58248691..58250268-chr15:58256342..58257981,2	K562	blood:
2	chr15:58245255..58247341-chr15:58247558..58249142,2	K562	blood:
3	chr15:58245255..58246964-chr15:58247558..58250422,2	K562	blood:

Variant related genes	Relation type
ALDH1A2	TF binding region
ENSG00000128918	Chromatin interaction

Extended variants
information (count: 118 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10518961	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs1061278	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1063666	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.89[TSI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10851632	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11071364	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs11071367	0.95[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap]
rs11631127	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11636979	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12148281	0.96[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12324197	0.81[ASN][1000 genomes]
rs12594082	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.82[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12595180	0.96[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes]
rs12898976	0.96[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12903724	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12905608	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12907038	0.84[CEU][hapmap]
rs12907125	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12909423	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12909865	0.85[EUR][1000 genomes]
rs12909979	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12912093	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs12914388	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12914455	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12914603	0.81[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs12915508	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12915821	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12915989	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12917536	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes]
rs1372369	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes]
rs1441815	0.95[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap]
rs1441819	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1441829	0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.85[EUR][1000 genomes]
rs17820966	0.95[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap]
rs17820990	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs1812889	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1822205	0.92[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.84[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1837851	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1899355	0.82[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap]
rs1994926	0.95[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap]
rs1994927	0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs2044071	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2067062	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs2119859	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2197092	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2414527	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2414529	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2414530	0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs2642630	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs2642632	0.82[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs2704218	0.85[GIH][hapmap]
rs2704225	0.81[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs2899611	0.95[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap]
rs2899613	0.95[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap]
rs3204690	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs33960206	0.86[EUR][1000 genomes]
rs34226780	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3742960	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3742961	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3784256	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3784257	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.82[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3784259	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3784263	0.87[LWK][hapmap]
rs3784264	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4144005	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs4238327	0.95[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap]
rs4646554	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs4646555	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs4646557	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs4646559	0.91[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs4646560	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs4646564	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs4646566	0.83[EUR][1000 genomes]
rs4646579	0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes]
rs4646580	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs4646581	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4646582	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs4646584	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4646588	0.82[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs4646589	0.82[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs4646590	0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4646592	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4646594	0.96[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4646595	0.96[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4646596	0.83[EUR][1000 genomes]
rs4646597	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4646598	0.84[EUR][1000 genomes]
rs4646600	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes]
rs4646602	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4646603	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4646605	0.82[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs4646606	0.81[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs4646607	0.82[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap]
rs4646609	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4646616	0.81[CEU][hapmap]
rs4646623	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4646625	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4646626	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4646635	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4646642	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.89[TSI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4646645	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4775006	0.85[AMR][1000 genomes]
rs57975858	0.81[ASN][1000 genomes]
rs6493977	0.95[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap]
rs6493979	0.95[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap]
rs6493980	0.83[EUR][1000 genomes]
rs6493981	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs7171261	0.92[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs7171714	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7178598	0.96[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7180059	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8026952	0.92[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes]
rs8027188	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs8032572	0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap];0.85[EUR][1000 genomes]
rs8041644	0.81[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.81[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	nsv1038667	chr15:57933076-58481870	Flanking Active TSS Enhancers Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv542400	chr15:57933076-58481870	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv833023	chr15:58161839-58340174	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv569593	chr15:58201698-58308650	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58240200-58252800	Weak transcription	Fetal Lung	lung
2	chr15:58243800-58253800	Weak transcription	Right Atrium	heart
3	chr15:58247000-58253600	Weak transcription	Fetal Heart	heart
4	chr15:58247400-58254000	Strong transcription	Fetal Kidney	kidney
5	chr15:58247600-58250400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr15:58248000-58253000	Weak transcription	Ovary	ovary
7	chr15:58248400-58249200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr15:58248600-58249200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr15:58248600-58249600	Enhancers	HMEC	breast
10	chr15:58248600-58249800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr15:58248800-58262400	Weak transcription	Fetal Muscle Leg	muscle
12	chr15:58249000-58249400	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr15:58249000-58259200	Strong transcription	K562	blood

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