Variant report

Variant	rs1536166
Chromosome Location	chr1:84427052-84427053
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:84401511..84403535-chr1:84426504..84429096,2	MCF-7	breast:

Extended variants
information (count: 125 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs10127737	0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10465746	0.93[ASN][1000 genomes]
rs10493741	0.87[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10493744	0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10874423	0.89[ASN][1000 genomes]
rs10874424	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11163861	0.87[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11163862	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11163865	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11163866	0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11163867	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11163868	0.87[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs11163872	0.83[ASN][1000 genomes]
rs11163874	0.86[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11163875	0.87[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11163876	0.94[ASN][1000 genomes]
rs11163877	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11163878	0.87[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11163879	0.97[ASN][1000 genomes]
rs11163884	0.96[ASN][1000 genomes]
rs11163885	0.96[ASN][1000 genomes]
rs11163886	0.96[ASN][1000 genomes]
rs11163887	0.96[ASN][1000 genomes]
rs11807807	0.94[ASN][1000 genomes]
rs12070578	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12118434	0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12119275	0.87[CHB][hapmap]
rs12121175	0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12127266	0.88[ASN][1000 genomes]
rs12133778	0.88[ASN][1000 genomes]
rs12135028	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12139191	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12140068	0.93[ASN][1000 genomes]
rs12141272	0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12145258	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12145516	0.95[ASN][1000 genomes]
rs12146038	0.87[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12184292	0.83[ASN][1000 genomes]
rs12401314	0.96[ASN][1000 genomes]
rs12402130	0.95[ASN][1000 genomes]
rs12403631	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12406984	0.92[ASN][1000 genomes]
rs12407641	0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12410398	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12410617	0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12723239	0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12730621	0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12732697	0.83[ASN][1000 genomes]
rs12738214	0.83[ASN][1000 genomes]
rs12748268	0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12749350	0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12757632	0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs12758441	0.83[ASN][1000 genomes]
rs12759527	0.87[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs1324484	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1324486	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1359331	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1475263	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs1536165	0.91[ASN][1000 genomes]
rs1570690	0.90[ASN][1000 genomes]
rs1570691	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17099118	1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[ASN][1000 genomes]
rs17475760	0.95[ASN][1000 genomes]
rs17534614	0.91[ASN][1000 genomes]
rs1871924	0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1871925	0.97[ASN][1000 genomes]
rs1886769	0.96[ASN][1000 genomes]
rs1886770	0.97[ASN][1000 genomes]
rs1925710	0.95[ASN][1000 genomes]
rs1952065	0.82[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1952066	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2024591	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2147392	0.89[ASN][1000 genomes]
rs2147950	0.82[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2224990	0.98[ASN][1000 genomes]
rs2389616	1.00[ASN][1000 genomes]
rs2389617	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs2389647	0.91[ASN][1000 genomes]
rs2389648	0.90[ASN][1000 genomes]
rs2389649	0.89[ASN][1000 genomes]
rs2477201	0.85[JPT][hapmap]
rs28445286	0.96[ASN][1000 genomes]
rs28567085	0.98[ASN][1000 genomes]
rs28726372	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs34155960	0.94[ASN][1000 genomes]
rs34274953	0.87[ASN][1000 genomes]
rs34636124	0.93[ASN][1000 genomes]
rs35485748	0.97[ASN][1000 genomes]
rs35946036	0.98[ASN][1000 genomes]
rs35969331	0.98[ASN][1000 genomes]
rs4258241	0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4907186	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4907188	0.83[ASN][1000 genomes]
rs4907189	0.87[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs4907190	0.94[ASN][1000 genomes]
rs4907191	0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs558567	0.85[JPT][hapmap]
rs575633	0.85[JPT][hapmap]
rs598531	0.85[JPT][hapmap]
rs639666	0.85[JPT][hapmap]
rs663136	0.85[JPT][hapmap]
rs6658559	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6667468	0.95[ASN][1000 genomes]
rs6670658	0.98[ASN][1000 genomes]
rs6685344	0.86[ASN][1000 genomes]
rs6687372	0.98[ASN][1000 genomes]
rs6692233	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6694752	0.82[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6699501	0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs670284	0.85[JPT][hapmap]
rs6703382	0.87[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6703493	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs685472	0.85[JPT][hapmap]
rs686839	0.85[JPT][hapmap]
rs7531537	0.96[ASN][1000 genomes]
rs7550413	0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs7551787	0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs882897	0.82[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs936661	0.90[ASN][1000 genomes]
rs942848	0.87[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs942849	0.98[ASN][1000 genomes]
rs9660265	0.97[ASN][1000 genomes]
rs980417	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs980418	0.87[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	nsv871551	chr1:84354464-84453223	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1536166	SSX2IP	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84368400-84428400	Weak transcription	Pancreas	Pancrea
2	chr1:84399200-84429800	Weak transcription	HSMMtube	muscle
3	chr1:84403600-84427400	Weak transcription	Fetal Brain Female	brain
4	chr1:84410400-84428000	Weak transcription	Brain Germinal Matrix	brain
5	chr1:84416400-84428400	Weak transcription	Aorta	Aorta
6	chr1:84416800-84436400	Weak transcription	Psoas Muscle	Psoas
7	chr1:84420400-84435800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr1:84423600-84428200	Enhancers	Brain Cingulate Gyrus	brain
9	chr1:84424600-84427600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:84424600-84427800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:84424800-84429000	Enhancers	Brain Substantia Nigra	brain
12	chr1:84425200-84433000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:84425200-84453200	Weak transcription	NHLF	lung
14	chr1:84425600-84427200	Enhancers	Brain Angular Gyrus	brain
15	chr1:84425800-84427800	Enhancers	HSMM	muscle
16	chr1:84426200-84427400	Enhancers	Stomach Mucosa	stomach
17	chr1:84426200-84452200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:84426400-84427400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr1:84426400-84427400	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr1:84426400-84428600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:84426400-84430000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:84426600-84431600	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr1:84426800-84427600	Weak transcription	NHDF-Ad	bronchial
24	chr1:84426800-84435800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr1:84427000-84427200	Flanking Active TSS	Brain Hippocampus Middle	brain
26	chr1:84427000-84430400	Enhancers	Brain Anterior Caudate	brain

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