Variant report

Variant	rs2486445
Chromosome Location	chr1:46605369-46605370
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:46603018..46605459-chr1:46613609..46615653,2	MCF-7	breast:
2	chr1:46594966..46603778-chr1:46605359..46614228,17	K562	blood:
3	chr1:46593944..46606364-chr1:46632700..46654752,92	MCF-7	breast:
4	chr1:46590920..46606215-chr1:46630948..46642525,66	MCF-7	breast:
5	chr1:46484546..46487489-chr1:46603817..46605793,2	K562	blood:
6	chr1:46501329..46503162-chr1:46604855..46606915,2	K562	blood:

Variant related genes	Relation type
ENSG00000250719	Chromatin interaction
ENSG00000117461	Chromatin interaction
ENSG00000117472	Chromatin interaction
ENSG00000227857	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 25 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10789487	0.84[CEU][hapmap];0.93[YRI][hapmap]
rs1085243	0.84[CEU][hapmap];0.87[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs1085244	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10890383	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs11211230	0.84[CEU][hapmap];0.93[YRI][hapmap]
rs11579634	0.84[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap];0.93[YRI][hapmap]
rs11589562	0.88[ASW][hapmap];0.81[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap]
rs11810993	0.88[ASW][hapmap];0.84[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap];0.93[YRI][hapmap]
rs12021587	0.84[CEU][hapmap];0.93[YRI][hapmap]
rs12049588	0.84[CEU][hapmap];0.96[YRI][hapmap]
rs12132540	0.87[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap]
rs1355642	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1707302	0.89[CHD][hapmap]
rs1707304	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1707308	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1707321	0.84[CEU][hapmap];0.87[CHB][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs1707333	0.82[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap]
rs1707334	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1707335	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1707336	0.88[ASW][hapmap];0.84[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap]
rs1707340	0.84[CEU][hapmap];0.87[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs1768803	0.80[ASN][1000 genomes]
rs1768809	0.89[GIH][hapmap]
rs1768816	0.84[CEU][hapmap];0.83[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs2275426	0.88[ASW][hapmap];0.84[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap];0.93[YRI][hapmap]
rs4073846	0.88[ASW][hapmap];0.84[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap];0.93[YRI][hapmap]
rs4076006	0.88[ASW][hapmap];0.84[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap];0.93[YRI][hapmap]
rs4660910	0.84[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap]
rs4660911	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6662641	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6675726	0.80[CEU][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7522601	0.84[CEU][hapmap];0.93[YRI][hapmap]
rs785464	0.84[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap]
rs785472	0.84[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap]
rs785473	0.84[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap]
rs785479	0.93[YRI][hapmap]
rs785481	0.84[CEU][hapmap];0.87[CHB][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs785485	0.84[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs785488	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs785489	0.84[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs785491	0.83[CEU][hapmap];0.86[CHB][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs785492	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs785494	0.84[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs785495	0.88[ASW][hapmap];0.84[CEU][hapmap];0.87[CHB][hapmap];0.80[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs785498	0.81[ASN][1000 genomes]
rs785502	0.84[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs785503	0.84[CEU][hapmap];0.83[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs785508	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs785509	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs785511	0.84[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap]
rs785520	0.84[CEU][hapmap];0.87[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs809774	0.85[JPT][hapmap]
rs809775	0.84[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap]
rs9429094	0.81[EUR][1000 genomes]
rs9429095	0.89[CHD][hapmap]
rs9429183	0.83[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap]
rs9429189	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs946529	0.84[CEU][hapmap];0.93[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
2	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers 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	232 gene(s)	inside rSNPs	diseases
3	nsv871928	chr1:46024701-46609736	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
4	nsv1003517	chr1:46244432-46609881	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
6	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
7	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
8	esv2754420	chr1:46461580-46635180	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv1006747	chr1:46476089-46655484	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
10	nsv534947	chr1:46476089-46655484	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
11	nsv1012418	chr1:46544842-46619890	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
12	nsv534948	chr1:46544842-46619890	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
13	nsv1006530	chr1:46544842-46655484	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
14	nsv534949	chr1:46544842-46655484	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:25)

SNP	Gene	Cis/trans	Tissue	Source
rs2486445	CCDC163P	cis	Whole Blood	GTEx
rs2486445	CCDC163P	cis	Esophagus Muscularis	GTEx
rs2486445	CCDC163P	cis	Heart Left Ventricle	GTEx
rs2486445	IPP	cis	lymphoblastoid	seeQTL
rs2486445	CCDC163P	cis	Thyroid	GTEx
rs2486445	CCDC163P	cis	Artery Aorta	GTEx
rs2486445	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx
rs2486445	CCDC163P	cis	Artery Tibial	GTEx
rs2486445	IPP	trans	brain	seeQTL
rs2486445	CYP4Z2P	cis	parietal	SCAN
rs2486445	CCDC163P	cis	Adipose Subcutaneous	GTEx
rs2486445	CCDC163P	cis	Muscle Skeletal	GTEx
rs2486445	IPP	cis	parietal	SCAN
rs2486445	MAST2	cis	cerebellum	SCAN
rs2486445	CCDC163P	cis	Stomach	GTEx
rs2486445	GPBP1L1	cis	Lymphoblastoid	GTEx
rs2486445	CYP4Z2P	cis	cerebellum	SCAN
rs2486445	IPP	cis	brain	seeQTL
rs2486445	LOC126661	Cis_1M	lymphoblastoid	RTeQTL
rs2486445	IPP	Cis_1M	lymphoblastoid	RTeQTL
rs2486445	MAST2	cis	Artery Tibial	GTEx
rs2486445	CCDC163P	cis	Esophagus Mucosa	GTEx
rs2486445	MAST2	cis	Artery Aorta	GTEx
rs2486445	CCDC163P	cis	Nerve Tibial	GTEx
rs2486445	CCDC163P	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46604000-46623600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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