Variant report

Variant	rs2991966
Chromosome Location	chr1:45999503-45999504
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:45990085..45992504-chr1:45996653..45999903,3	MCF-7	breast:
2	chr1:45998915..46004761-chr1:46006522..46011880,8	K562	blood:

Extended variants
information (count: 84 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1006215	1.00[JPT][hapmap]
rs10157597	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1044717	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10493120	0.81[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs10736426	0.91[CEU][hapmap];0.96[GIH][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10789466	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1088099	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11211110	0.81[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs11211113	0.86[GIH][hapmap];1.00[MEX][hapmap]
rs11211115	1.00[JPT][hapmap]
rs11211132	0.91[CEU][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11211133	1.00[ASN][1000 genomes]
rs11211134	0.92[EUR][1000 genomes]
rs11211138	0.83[EUR][1000 genomes]
rs12021717	1.00[ASN][1000 genomes]
rs12038608	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12042481	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12047498	0.88[ASN][1000 genomes]
rs12048936	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12082256	0.87[EUR][1000 genomes]
rs12145526	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12729974	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12749658	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1337902	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1494813	0.95[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1691217	0.86[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap]
rs1771549	1.00[JPT][hapmap]
rs1974271	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2065708	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2077808	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2152077	0.91[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2356555	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2356559	0.91[CEU][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs2356560	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2356561	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2993257	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2993259	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34315657	0.81[EUR][1000 genomes]
rs3748643	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3748644	1.00[JPT][hapmap]
rs4233498	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4660306	0.91[CEU][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4660309	0.87[EUR][1000 genomes]
rs4660860	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4660862	0.95[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4660864	0.95[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4660866	0.84[EUR][1000 genomes]
rs4660867	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4660868	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4660871	0.82[EUR][1000 genomes]
rs4660872	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6429566	0.86[GIH][hapmap];0.89[MEX][hapmap]
rs6429567	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6429569	0.91[CEU][hapmap];0.96[GIH][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6667191	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6673477	0.85[EUR][1000 genomes]
rs6688424	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6688516	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7516006	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7522705	0.91[CEU][hapmap];0.96[GIH][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7534467	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7536557	0.91[CEU][hapmap];0.96[GIH][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7539253	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7543076	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7546268	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7549093	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs781057	1.00[JPT][hapmap]
rs781059	0.84[GIH][hapmap];1.00[MEX][hapmap]
rs781060	0.86[GIH][hapmap];1.00[MEX][hapmap]
rs781062	1.00[JPT][hapmap]
rs781066	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs882803	0.91[CEU][hapmap];0.96[GIH][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs937290	0.95[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs945179	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9725380	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9803979	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
3	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
4	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
5	nsv829726	chr1:45897581-46103186	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
6	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
7	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
8	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

mRNA abundance (count:22)

SNP	Gene	Cis/trans	Tissue	Source
rs2991966	CCDC163P	cis	lymphoblastoid	seeQTL
rs2991966	CCDC163P	cis	Artery Tibial	GTEx
rs2991966	TESK2	cis	lymphoblastoid	seeQTL
rs2991966	CCDC163P	cis	Whole Blood	GTEx
rs2991966	CYP4A11	cis	parietal	SCAN
rs2991966	CCDC163P	cis	Adipose Subcutaneous	GTEx
rs2991966	CCDC163P	cis	Muscle Skeletal	GTEx
rs2991966	CCDC163P	cis	lung	GTEx
rs2991966	CCDC163P	cis	Esophagus Muscularis	GTEx
rs2991966	CCDC163P	cis	Heart Left Ventricle	GTEx
rs2991966	BEND5	cis	cerebellum	SCAN
rs2991966	CCDC163P	cis	Nerve Tibial	GTEx
rs2991966	CYP4Z2P	cis	parietal	SCAN
rs2991966	CCDC163P	cis	Artery Aorta	GTEx
rs2991966	CCDC163P	cis	Esophagus Mucosa	GTEx
rs2991966	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx
rs2991966	ST3GAL3	cis	parietal	SCAN
rs2991966	TESK2	cis	multi-tissue	Pritchard
rs2991966	LOC126661	cis	uninvolved skin	skin_eQTL
rs2991966	CCDC163P	cis	Thyroid	GTEx
rs2991966	CCDC163P	cis	Stomach	GTEx
rs2991966	LOC126661	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45989200-46000600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:45992800-46002400	Weak transcription	Fetal Intestine Small	intestine
3	chr1:45998600-45999800	Enhancers	HepG2	liver
4	chr1:45999200-45999800	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr1:45999200-46004600	Weak transcription	Monocytes-CD14+_RO01746	blood

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