Variant report

Variant	rs663136
Chromosome Location	chr1:84437311-84437312
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10127737	0.85[JPT][hapmap]
rs10493741	0.85[JPT][hapmap]
rs10493744	0.85[JPT][hapmap]
rs10874424	0.84[JPT][hapmap]
rs11163861	0.85[JPT][hapmap]
rs11163862	0.85[JPT][hapmap]
rs11163865	0.85[JPT][hapmap]
rs11163866	0.85[JPT][hapmap]
rs11163867	0.85[JPT][hapmap]
rs11163868	0.80[JPT][hapmap]
rs11163874	0.89[JPT][hapmap]
rs11163875	0.85[JPT][hapmap]
rs11163877	0.83[JPT][hapmap]
rs11163878	0.89[JPT][hapmap]
rs12070578	0.85[JPT][hapmap]
rs12118434	0.85[JPT][hapmap]
rs12121175	0.85[JPT][hapmap]
rs12135028	0.85[JPT][hapmap]
rs12139191	0.85[JPT][hapmap]
rs12141272	0.85[JPT][hapmap]
rs12145258	0.85[JPT][hapmap]
rs12146038	0.84[JPT][hapmap]
rs12403631	0.85[JPT][hapmap]
rs12407641	0.85[JPT][hapmap]
rs12410617	0.85[JPT][hapmap]
rs12723239	0.85[JPT][hapmap]
rs12730621	0.85[JPT][hapmap]
rs12748268	0.85[JPT][hapmap]
rs12749350	0.85[JPT][hapmap]
rs12759527	0.80[JPT][hapmap]
rs1324484	0.89[JPT][hapmap]
rs1324486	0.85[JPT][hapmap]
rs1359331	0.85[JPT][hapmap]
rs1475263	0.85[JPT][hapmap]
rs1536166	0.85[JPT][hapmap]
rs1570691	0.85[JPT][hapmap]
rs17099118	0.85[JPT][hapmap]
rs17475438	0.84[CEU][hapmap]
rs1871924	0.85[JPT][hapmap]
rs1952065	0.85[JPT][hapmap]
rs1952066	0.85[JPT][hapmap]
rs2024591	0.85[JPT][hapmap]
rs2147950	0.85[JPT][hapmap]
rs2389617	0.88[JPT][hapmap]
rs2477201	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap]
rs4258241	0.85[JPT][hapmap]
rs4907186	0.85[JPT][hapmap]
rs4907191	0.85[JPT][hapmap]
rs558567	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs575633	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap]
rs598531	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs639666	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6658559	0.85[JPT][hapmap]
rs6692233	0.85[JPT][hapmap]
rs6694752	0.85[JPT][hapmap]
rs6699501	0.83[JPT][hapmap]
rs670284	0.94[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs6703382	0.85[JPT][hapmap]
rs6703493	0.88[JPT][hapmap]
rs685472	0.94[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs686839	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7550413	0.83[JPT][hapmap]
rs7551787	0.85[JPT][hapmap]
rs882897	0.80[JPT][hapmap]
rs942848	0.85[JPT][hapmap]
rs980417	0.85[JPT][hapmap]

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
rs663136	LPHN2	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84425200-84453200	Weak transcription	NHLF	lung
2	chr1:84426200-84452200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:84427800-84444600	Weak transcription	HSMM	muscle
4	chr1:84429200-84445400	Weak transcription	Aorta	Aorta
5	chr1:84430200-84441600	Weak transcription	HSMMtube	muscle
6	chr1:84430400-84447400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:84431600-84437400	Enhancers	Brain Substantia Nigra	brain
8	chr1:84433800-84446000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:84436000-84437400	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr1:84436400-84437400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:84436400-84440400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr1:84436600-84452200	Weak transcription	Brain Angular Gyrus	brain
13	chr1:84436800-84440400	Weak transcription	Psoas Muscle	Psoas
14	chr1:84436800-84444800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr1:84437000-84439400	Weak transcription	Fetal Brain Female	brain
16	chr1:84437200-84440600	Weak transcription	Brain Hippocampus Middle	brain

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