Variant report

Variant	rs12406984
Chromosome Location	chr1:84416215-84416216
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 120 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs10127737	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10465746	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10493741	0.93[CEU][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10493744	1.00[CEU][hapmap];0.92[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10874423	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10874424	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11163861	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11163862	0.89[CEU][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11163865	0.89[CEU][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11163866	0.89[CEU][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11163867	0.85[CEU][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11163868	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11163872	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11163874	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11163875	1.00[CEU][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11163876	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11163877	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11163878	0.96[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11163879	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11163884	0.91[ASN][1000 genomes]
rs11163885	0.91[ASN][1000 genomes]
rs11163886	0.91[ASN][1000 genomes]
rs11163887	0.91[ASN][1000 genomes]
rs11576870	0.85[EUR][1000 genomes]
rs11580836	0.85[EUR][1000 genomes]
rs11807807	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12070578	0.81[ASN][1000 genomes]
rs12118434	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs12120160	0.86[EUR][1000 genomes]
rs12121175	0.92[ASN][1000 genomes]
rs12127266	0.87[AFR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12133778	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12135028	0.88[ASN][1000 genomes]
rs12139191	0.89[CEU][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12140068	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12141272	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12145258	0.89[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12145516	0.90[ASN][1000 genomes]
rs12146038	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12184292	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12401314	0.91[ASN][1000 genomes]
rs12402130	0.90[ASN][1000 genomes]
rs12403631	0.90[ASN][1000 genomes]
rs12407641	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12410398	0.92[ASN][1000 genomes]
rs12410617	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12723239	0.93[ASN][1000 genomes]
rs12730621	0.89[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12732697	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12738214	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12748268	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12749350	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12757632	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12758441	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12759527	1.00[CEU][hapmap];0.92[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1324484	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1324486	0.89[CEU][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1359331	0.81[CEU][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1475263	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs1536165	0.87[ASN][1000 genomes]
rs1536166	0.92[ASN][1000 genomes]
rs1570690	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1570691	0.89[CEU][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17099118	0.90[ASN][1000 genomes]
rs17475760	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17534614	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1871924	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1871925	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1886769	0.92[ASN][1000 genomes]
rs1886770	0.93[ASN][1000 genomes]
rs1925710	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1952065	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1952066	0.89[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2147392	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2147950	0.92[ASN][1000 genomes]
rs2224990	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2389616	0.92[ASN][1000 genomes]
rs2389617	0.93[CEU][hapmap]
rs2389647	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2389648	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2389649	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28445286	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28567085	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28726372	0.80[ASN][1000 genomes]
rs34155960	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34274953	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs34636124	0.89[ASN][1000 genomes]
rs35485748	0.93[ASN][1000 genomes]
rs35946036	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35969331	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4258241	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4907188	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4907189	0.96[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4907190	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4907191	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5028806	0.85[EUR][1000 genomes]
rs6576956	0.86[EUR][1000 genomes]
rs6658559	0.92[ASN][1000 genomes]
rs6663949	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6667468	0.90[ASN][1000 genomes]
rs6670658	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6685344	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6687372	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6692233	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs6694752	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6699501	0.85[CEU][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6703382	1.00[CEU][hapmap];0.93[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6703493	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7531537	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7550413	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7551787	0.88[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs882897	0.89[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs936661	0.86[ASN][1000 genomes]
rs942848	1.00[CEU][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs942849	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9660265	0.93[ASN][1000 genomes]
rs9700285	0.85[EUR][1000 genomes]
rs980417	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs980418	0.80[EUR][1000 genomes];0.86[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

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84368400-84416600	Weak transcription	NHLF	lung
2	chr1:84368400-84428400	Weak transcription	Pancreas	Pancrea
3	chr1:84392200-84422400	Weak transcription	Fetal Stomach	stomach
4	chr1:84392400-84420400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr1:84399200-84429800	Weak transcription	HSMMtube	muscle
6	chr1:84403600-84426200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr1:84403600-84427400	Weak transcription	Fetal Brain Female	brain
8	chr1:84407400-84416400	Weak transcription	Brain Substantia Nigra	brain
9	chr1:84407800-84416400	Weak transcription	Brain Angular Gyrus	brain
10	chr1:84409400-84420000	Weak transcription	Fetal Muscle Leg	muscle
11	chr1:84409600-84424400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:84410400-84425400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:84410400-84426400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:84410400-84428000	Weak transcription	Brain Germinal Matrix	brain
15	chr1:84410600-84426400	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr1:84411400-84417800	Weak transcription	Brain Anterior Caudate	brain
17	chr1:84413800-84416400	Weak transcription	Psoas Muscle	Psoas
18	chr1:84415800-84416400	Active TSS	Aorta	Aorta
19	chr1:84415800-84416400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr1:84415800-84416800	Enhancers	Brain Cingulate Gyrus	brain
21	chr1:84416000-84416400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:84416000-84416400	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr1:84416000-84416400	Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr1:84416200-84416600	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr1:84416200-84416800	Enhancers	Brain Hippocampus Middle	brain
26	chr1:84416200-84416800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr1:84416200-84425800	Weak transcription	HSMM	muscle

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