Variant report

Variant	rs670284
Chromosome Location	chr1:84340194-84340195
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10127737	0.85[JPT][hapmap]
rs10493741	0.85[JPT][hapmap]
rs10493744	0.85[JPT][hapmap]
rs10874424	0.84[JPT][hapmap]
rs11163858	0.84[EUR][1000 genomes]
rs11163859	0.85[EUR][1000 genomes]
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]
rs1132122	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
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	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4258241	0.85[JPT][hapmap]
rs4907186	0.85[JPT][hapmap]
rs4907191	0.85[JPT][hapmap]
rs558567	0.94[ASW][hapmap];1.00[CEU][hapmap];0.82[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];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs575633	0.88[ASW][hapmap];0.83[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs598531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs639666	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs663136	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]
rs6658559	0.85[JPT][hapmap]
rs6692233	0.85[JPT][hapmap]
rs6694752	0.85[JPT][hapmap]
rs6699501	0.83[JPT][hapmap]
rs6703382	0.85[JPT][hapmap]
rs6703493	0.88[JPT][hapmap]
rs685472	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs686839	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];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
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	nsv947282	chr1:84338235-84350669	Enhancers Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs670284	LPHN2	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84326800-84348200	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr1:84326800-84352600	Weak transcription	Fetal Muscle Trunk	muscle
3	chr1:84327000-84345000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:84327000-84348400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:84327000-84352400	Weak transcription	Aorta	Aorta
6	chr1:84327000-84361800	Weak transcription	Fetal Brain Female	brain
7	chr1:84327000-84375400	Weak transcription	Brain Germinal Matrix	brain
8	chr1:84327200-84348600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr1:84327200-84349600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:84327200-84351400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr1:84327400-84345000	Weak transcription	Brain Anterior Caudate	brain
12	chr1:84328200-84354400	Weak transcription	Brain Substantia Nigra	brain
13	chr1:84328800-84344800	Weak transcription	Brain Hippocampus Middle	brain
14	chr1:84329000-84352200	Weak transcription	Brain Angular Gyrus	brain
15	chr1:84329000-84373000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr1:84331000-84352400	Weak transcription	Fetal Muscle Leg	muscle
17	chr1:84331400-84348000	Weak transcription	HSMM	muscle
18	chr1:84333400-84382400	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr1:84334600-84355400	Weak transcription	HSMMtube	muscle
20	chr1:84334800-84342600	Weak transcription	NHLF	lung
21	chr1:84335800-84352400	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr1:84336400-84349600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:84338600-84348200	Weak transcription	Liver	Liver
24	chr1:84338800-84367600	Weak transcription	Pancreas	Pancrea

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