Variant report

Variant	rs2477201
Chromosome Location	chr1:84390526-84390527
allele	G/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]
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	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[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]
rs4258241	0.85[JPT][hapmap]
rs4907186	0.85[JPT][hapmap]
rs4907191	0.85[JPT][hapmap]
rs558567	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs575633	0.93[ASW][hapmap];0.83[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs587007	0.83[ASN][1000 genomes]
rs598531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs639666	0.83[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes]
rs657134	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs663136	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]
rs6658559	0.85[JPT][hapmap]
rs6692233	0.85[JPT][hapmap]
rs6694752	0.85[JPT][hapmap]
rs6699501	0.83[JPT][hapmap]
rs670284	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]
rs6703382	0.85[JPT][hapmap]
rs6703493	0.88[JPT][hapmap]
rs685472	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];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs686839	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];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][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	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
rs2477201	LPHN2	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84351000-84391400	Weak transcription	Fetal Stomach	stomach
2	chr1:84362600-84403200	Weak transcription	Fetal Brain Male	brain
3	chr1:84366400-84392800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr1:84366800-84399400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr1:84368000-84394200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:84368200-84393400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:84368200-84393800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr1:84368200-84394800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:84368400-84416600	Weak transcription	NHLF	lung
10	chr1:84368400-84428400	Weak transcription	Pancreas	Pancrea
11	chr1:84374200-84393000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:84376200-84392800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:84376800-84405000	Weak transcription	Left Ventricle	heart
14	chr1:84380800-84392200	Weak transcription	NHEK	skin
15	chr1:84381000-84393400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr1:84381000-84394800	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr1:84381000-84397400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:84382600-84409800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:84383200-84393000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:84383200-84408600	Weak transcription	Adipose Nuclei	Adipose
21	chr1:84383400-84391000	Weak transcription	Brain Angular Gyrus	brain
22	chr1:84384800-84406600	Weak transcription	Aorta	Aorta
23	chr1:84385000-84392200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr1:84385000-84392400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:84385000-84392800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr1:84385000-84393200	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr1:84385200-84408600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:84386200-84393800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:84386200-84397800	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr1:84386600-84391000	Weak transcription	Brain Hippocampus Middle	brain
31	chr1:84386600-84392800	Weak transcription	Brain Substantia Nigra	brain
32	chr1:84386600-84392800	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr1:84386600-84401600	Weak transcription	Stomach Smooth Muscle	stomach
34	chr1:84386800-84392000	Weak transcription	Brain Anterior Caudate	brain
35	chr1:84386800-84398400	Weak transcription	HSMMtube	muscle
36	chr1:84386800-84398800	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr1:84386800-84403200	Weak transcription	NHDF-Ad	bronchial
38	chr1:84387000-84408400	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr1:84387000-84408400	Weak transcription	Fetal Muscle Leg	muscle
40	chr1:84387000-84410000	Weak transcription	Brain Germinal Matrix	brain
41	chr1:84388200-84391000	Weak transcription	Gastric	stomach
42	chr1:84388800-84402200	Weak transcription	HSMM	muscle
43	chr1:84389600-84391200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:84389800-84390600	Strong transcription	Fetal Brain Female	brain
45	chr1:84390000-84392400	Strong transcription	Fetal Muscle Trunk	muscle
46	chr1:84390200-84393400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr1:84390200-84397600	Weak transcription	K562	blood

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