Variant report

Variant	rs781226
Chromosome Location	chr1:45872662-45872663
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:45870070..45872383-chr1:45872403..45873917,2	MCF-7	breast:

Extended variants
information (count: 108 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs1006216	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1007858	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10789463	0.81[CHD][hapmap]
rs10789464	0.80[EUR][1000 genomes]
rs10789465	0.83[CHB][hapmap]
rs1084166	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10890327	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10890330	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11211101	0.86[CEU][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.91[EUR][1000 genomes]
rs11211108	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11211111	0.95[CEU][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11211117	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11211118	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11211123	0.80[EUR][1000 genomes]
rs11211124	0.81[CEU][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs12029322	0.81[CEU][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs12037201	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12037411	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12046816	0.95[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12049503	0.81[CEU][hapmap];0.81[MEX][hapmap]
rs12067642	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12097497	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12139364	0.83[CHB][hapmap];0.81[CHD][hapmap];0.87[JPT][hapmap]
rs12410493	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12564806	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12738318	0.83[CHB][hapmap];0.81[CHD][hapmap]
rs12743512	0.83[CHB][hapmap]
rs1417578	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1494812	0.94[CEU][hapmap];0.84[CHB][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1538970	0.80[EUR][1000 genomes]
rs17395553	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1771551	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1826691	0.95[CEU][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2050884	0.94[ASW][hapmap];0.86[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.96[YRI][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2055145	0.91[CEU][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2088100	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2153607	0.94[ASW][hapmap];0.86[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.93[YRI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2153608	0.94[ASW][hapmap];0.86[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.93[YRI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2153609	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs2185549	0.86[CEU][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.86[EUR][1000 genomes]
rs2275276	0.83[CHB][hapmap]
rs2298018	0.94[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.93[YRI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2487442	0.94[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2492836	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2492840	0.94[ASW][hapmap];0.86[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.96[YRI][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28555082	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3219463	0.86[CEU][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.85[EUR][1000 genomes]
rs3219472	0.86[CEU][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.85[EUR][1000 genomes]
rs3219489	0.86[CEU][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes]
rs3790582	0.95[CEU][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3790583	0.80[EUR][1000 genomes]
rs4520450	0.86[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap]
rs4633317	0.81[CEU][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap]
rs4660301	0.86[EUR][1000 genomes]
rs4660849	0.86[CEU][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.87[EUR][1000 genomes]
rs4660851	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4660852	0.86[CEU][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.91[EUR][1000 genomes]
rs4660853	0.86[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4660854	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4660855	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4660858	0.95[CEU][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4660863	0.81[CEU][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs55642258	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61788261	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61788262	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61788281	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61788285	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61791362	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61791368	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61791369	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6657284	0.95[CEU][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs6670303	0.83[ASN][1000 genomes]
rs713358	0.81[CEU][hapmap]
rs72686460	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7417107	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7525849	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7528573	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7531253	0.95[CEU][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7532762	0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7536135	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7543428	0.86[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7544178	0.86[CEU][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.87[EUR][1000 genomes]
rs7553318	0.86[CEU][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.91[EUR][1000 genomes]
rs781058	0.83[CHB][hapmap];0.81[CHD][hapmap]
rs781230	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs781232	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs868351	0.81[CEU][hapmap];0.83[TSI][hapmap]
rs884962	0.80[CEU][hapmap];0.91[EUR][1000 genomes]
rs9326141	0.86[CEU][hapmap];0.90[CHD][hapmap];0.90[EUR][1000 genomes]
rs937291	0.83[CHB][hapmap]
rs9429072	0.86[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap];0.85[YRI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9429073	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9429074	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9429076	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9429158	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9429159	0.87[EUR][1000 genomes]
rs9429160	0.86[CEU][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.89[EUR][1000 genomes]
rs9429161	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs998199	0.81[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1014509	chr1:45687523-45887501	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv997548	chr1:45733596-45955845	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv534942	chr1:45733596-45955845	Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv482356	chr1:45750459-45915545	Enhancers Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
6	esv2750837	chr1:45796115-45908263	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
7	esv1795802	chr1:45819489-46009818	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
8	esv1831217	chr1:45819489-46009818	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
9	nsv530016	chr1:45868543-46069020	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs781226	IPP	cis	lymphoblastoid	seeQTL
rs781226	MAST2	cis	cerebellum	SCAN
rs781226	MMACHC	cis	multi-tissue	Pritchard
rs781226	SPATA19	trans	parietal	SCAN
rs781226	CLDN19	cis	cerebellum	SCAN
rs781226	MUTYH	Cis_1M	lymphoblastoid	RTeQTL
rs781226	ST3GAL3	cis	parietal	SCAN
rs781226	C2orf49	trans	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45841400-45889200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:45861200-45874600	Weak transcription	GM12878-XiMat	blood
3	chr1:45869400-45885400	Weak transcription	Fetal Intestine Small	intestine
4	chr1:45869600-45874800	Weak transcription	HepG2	liver
5	chr1:45870200-45873600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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