Variant report

Variant	rs12070578
Chromosome Location	chr1:84349607-84349608
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 130 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:129)

rs_ID	r²[population]
rs10127737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10465746	0.89[ASN][1000 genomes]
rs10493741	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10493744	0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.84[ASN][1000 genomes]
rs10874423	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10874424	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10874426	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.88[EUR][1000 genomes]
rs11163861	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11163862	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11163865	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11163866	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11163867	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11163868	0.94[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs11163872	0.80[EUR][1000 genomes]
rs11163874	0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11163875	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11163876	0.81[ASN][1000 genomes]
rs11163877	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11163878	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11163879	0.83[ASN][1000 genomes]
rs11163884	0.83[ASN][1000 genomes]
rs11163885	0.83[ASN][1000 genomes]
rs11163886	0.83[ASN][1000 genomes]
rs11163887	0.83[ASN][1000 genomes]
rs11576870	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11580836	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12118434	0.94[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12119275	0.94[CHB][hapmap]
rs12120160	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12121175	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12127266	0.94[ASN][1000 genomes]
rs12133778	0.94[ASN][1000 genomes]
rs12135028	0.81[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12139191	0.83[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12140068	0.89[ASN][1000 genomes]
rs12141272	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12145258	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12145516	0.82[ASN][1000 genomes]
rs12146038	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12184292	0.83[ASN][1000 genomes]
rs12401314	0.81[ASN][1000 genomes]
rs12402130	0.82[ASN][1000 genomes]
rs12403631	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12406984	0.81[ASN][1000 genomes]
rs12407641	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12410398	0.82[ASN][1000 genomes]
rs12410617	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12723239	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12730621	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12732697	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12738214	0.89[ASN][1000 genomes]
rs12748268	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12749350	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12757632	0.90[GIH][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs12758441	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12759527	0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.84[ASN][1000 genomes]
rs1324484	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1324486	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1359331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1475263	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1536166	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1570690	0.89[ASN][1000 genomes]
rs1570691	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17099118	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs17475760	0.87[ASN][1000 genomes]
rs17534614	0.90[ASN][1000 genomes]
rs1871924	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1871925	0.83[ASN][1000 genomes]
rs1886769	0.84[ASN][1000 genomes]
rs1886770	0.83[ASN][1000 genomes]
rs1925710	0.87[ASN][1000 genomes]
rs1952065	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1952066	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2024591	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2147392	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2147950	1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2224990	0.84[ASN][1000 genomes]
rs2389616	0.82[ASN][1000 genomes]
rs2389617	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2389647	0.84[ASN][1000 genomes]
rs2389648	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2389649	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2477201	0.85[JPT][hapmap]
rs28445286	0.82[ASN][1000 genomes]
rs28567085	0.84[ASN][1000 genomes]
rs28726372	0.97[ASN][1000 genomes]
rs34155960	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35485748	0.83[ASN][1000 genomes]
rs35946036	0.84[ASN][1000 genomes]
rs35969331	0.84[ASN][1000 genomes]
rs4258241	0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4907185	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4907186	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4907188	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4907189	0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs4907190	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4907191	0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.84[ASN][1000 genomes]
rs5028806	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs558567	0.85[JPT][hapmap]
rs575633	0.85[JPT][hapmap]
rs598531	0.85[JPT][hapmap]
rs639666	0.85[JPT][hapmap]
rs6576956	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs663136	0.85[JPT][hapmap]
rs6658559	1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6663949	0.82[EUR][1000 genomes]
rs6667468	0.81[ASN][1000 genomes]
rs6670658	0.84[ASN][1000 genomes]
rs6685344	0.80[ASN][1000 genomes]
rs6687372	0.84[ASN][1000 genomes]
rs6692233	0.82[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6694752	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6699501	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs670284	0.85[JPT][hapmap]
rs6703382	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6703493	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs685472	0.85[JPT][hapmap]
rs686839	0.85[JPT][hapmap]
rs7529293	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7531537	0.85[ASN][1000 genomes]
rs7550413	0.81[CEU][hapmap];0.80[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7551787	0.81[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs882897	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs942848	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs942849	0.84[ASN][1000 genomes]
rs9660265	0.83[ASN][1000 genomes]
rs9700285	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs980417	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs980418	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12070578	LPHN2	cis	parietal	SCAN
rs12070578	NKX1-2	trans	parietal	SCAN
rs12070578	DNASE2B	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84326800-84352600	Weak transcription	Fetal Muscle Trunk	muscle
2	chr1:84327000-84352400	Weak transcription	Aorta	Aorta
3	chr1:84327000-84361800	Weak transcription	Fetal Brain Female	brain
4	chr1:84327000-84375400	Weak transcription	Brain Germinal Matrix	brain
5	chr1:84327200-84351400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr1:84328200-84354400	Weak transcription	Brain Substantia Nigra	brain
7	chr1:84329000-84352200	Weak transcription	Brain Angular Gyrus	brain
8	chr1:84329000-84373000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr1:84331000-84352400	Weak transcription	Fetal Muscle Leg	muscle
10	chr1:84333400-84382400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr1:84334600-84355400	Weak transcription	HSMMtube	muscle
12	chr1:84335800-84352400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr1:84338800-84367600	Weak transcription	Pancreas	Pancrea
14	chr1:84341000-84359400	Weak transcription	Psoas Muscle	Psoas
15	chr1:84341200-84380400	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr1:84343600-84361800	Weak transcription	Fetal Brain Male	brain
17	chr1:84345600-84384400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:84345800-84353800	Weak transcription	Brain Hippocampus Middle	brain
19	chr1:84346800-84382400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:84348200-84349800	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr1:84348200-84349800	Strong transcription	Brain Anterior Caudate	brain
22	chr1:84348400-84349800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:84348400-84349800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr1:84348400-84350000	Enhancers	NHDF-Ad	bronchial
25	chr1:84348400-84350200	Enhancers	Pancreatic Islets	Pancreatic Islet
26	chr1:84348400-84350200	Enhancers	NHEK	skin
27	chr1:84348600-84349800	Strong transcription	Stomach Smooth Muscle	stomach
28	chr1:84348600-84352000	Weak transcription	HSMM	muscle
29	chr1:84349000-84350200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr1:84349200-84349800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:84349200-84355200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:84349600-84350000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:84349600-84350000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:84349600-84350200	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr1:84349600-84350200	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr1:84349600-84352800	Weak transcription	Colon Smooth Muscle	Colon

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