Variant report

Variant	rs6694752
Chromosome Location	chr1:84389960-84389961
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:84388469..84390002-chr1:84396047..84397947,2	K562	blood:

Extended variants
information (count: 136 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:134)

rs_ID	r²[population]
rs10127737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10465746	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10493741	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10493744	0.94[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10874423	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10874424	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10874426	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11163861	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11163862	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11163865	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11163866	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11163867	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11163868	0.94[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11163872	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11163874	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11163875	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11163876	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11163877	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11163878	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11163879	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11163884	0.93[ASN][1000 genomes]
rs11163885	0.93[ASN][1000 genomes]
rs11163886	0.93[ASN][1000 genomes]
rs11163887	0.93[ASN][1000 genomes]
rs11576870	0.80[ASN][1000 genomes]
rs11580836	0.80[ASN][1000 genomes]
rs11807807	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12070578	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]
rs12118434	0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.80[ASN][1000 genomes]
rs12119275	0.94[CHB][hapmap]
rs12120160	0.80[ASN][1000 genomes]
rs12121175	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12127266	0.94[ASN][1000 genomes]
rs12133778	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12135028	0.81[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12139191	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12140068	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12141272	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12145258	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12145516	0.92[ASN][1000 genomes]
rs12146038	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12184292	0.89[ASN][1000 genomes]
rs12401314	0.91[ASN][1000 genomes]
rs12402130	0.92[ASN][1000 genomes]
rs12403631	0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12406984	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12407641	0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12410398	0.92[ASN][1000 genomes]
rs12410617	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12723239	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12730621	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12732697	0.89[ASN][1000 genomes]
rs12738214	0.89[ASN][1000 genomes]
rs12748268	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12749350	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12757632	0.90[GIH][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12758441	0.89[ASN][1000 genomes]
rs12759527	0.94[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1324484	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1324486	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1359331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1475263	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1536165	0.86[ASN][1000 genomes]
rs1536166	0.82[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1570690	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1570691	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17099118	0.82[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17475760	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17534614	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1871924	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1871925	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1886769	0.94[ASN][1000 genomes]
rs1886770	0.93[ASN][1000 genomes]
rs1925710	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1952065	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1952066	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2024591	0.94[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];0.92[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2147392	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2147950	1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2224990	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2389616	0.92[ASN][1000 genomes]
rs2389617	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2389647	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2389648	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2389649	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2477201	0.85[JPT][hapmap]
rs28445286	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28567085	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28726372	0.87[ASN][1000 genomes]
rs34155960	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34274953	0.86[ASN][1000 genomes]
rs34636124	0.89[ASN][1000 genomes]
rs35485748	0.93[ASN][1000 genomes]
rs35946036	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35969331	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4258241	0.94[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4907185	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4907186	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4907188	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4907189	0.94[CHB][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4907190	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4907191	0.94[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5028806	0.80[ASN][1000 genomes]
rs558567	0.85[JPT][hapmap]
rs575633	0.85[JPT][hapmap]
rs598531	0.85[JPT][hapmap]
rs639666	0.85[JPT][hapmap]
rs6576956	0.80[ASN][1000 genomes]
rs663136	0.85[JPT][hapmap]
rs6658559	1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6663949	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6667468	0.90[ASN][1000 genomes]
rs6670658	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6685344	0.90[ASN][1000 genomes]
rs6687372	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6692233	0.82[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs6699501	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs670284	0.85[JPT][hapmap]
rs6703382	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6703493	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs685472	0.85[JPT][hapmap]
rs686839	0.85[JPT][hapmap]
rs7529293	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7531537	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7550413	0.81[CEU][hapmap];0.80[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7551787	0.82[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];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs882897	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs936661	0.86[ASN][1000 genomes]
rs942848	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs942849	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9660265	0.93[ASN][1000 genomes]
rs9700285	0.80[ASN][1000 genomes]
rs980417	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs980418	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	esv3492575	chr1:84387164-84390162	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6694752	NKX1-2	trans	parietal	SCAN
rs6694752	LPHN2	cis	parietal	SCAN
rs6694752	DNASE2B	cis	cerebellum	SCAN

Chromatin state (count:50 , 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	chr1:84368000-84390000	Weak transcription	NH-A	brain
6	chr1:84368000-84394200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:84368200-84393400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:84368200-84393800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr1:84368200-84394800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:84368400-84416600	Weak transcription	NHLF	lung
11	chr1:84368400-84428400	Weak transcription	Pancreas	Pancrea
12	chr1:84374200-84393000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:84376200-84392800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:84376800-84405000	Weak transcription	Left Ventricle	heart
15	chr1:84378600-84390200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:84380800-84392200	Weak transcription	NHEK	skin
17	chr1:84381000-84393400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr1:84381000-84394800	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr1:84381000-84397400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:84381200-84390000	Weak transcription	Psoas Muscle	Psoas
21	chr1:84382600-84409800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:84383200-84393000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:84383200-84408600	Weak transcription	Adipose Nuclei	Adipose
24	chr1:84383400-84391000	Weak transcription	Brain Angular Gyrus	brain
25	chr1:84384800-84406600	Weak transcription	Aorta	Aorta
26	chr1:84385000-84392200	Weak transcription	Brain Cingulate Gyrus	brain
27	chr1:84385000-84392400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr1:84385000-84392800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr1:84385000-84393200	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr1:84385200-84390000	Weak transcription	Fetal Muscle Trunk	muscle
31	chr1:84385200-84408600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:84386200-84393800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr1:84386200-84397800	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr1:84386600-84391000	Weak transcription	Brain Hippocampus Middle	brain
35	chr1:84386600-84392800	Weak transcription	Brain Substantia Nigra	brain
36	chr1:84386600-84392800	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr1:84386600-84401600	Weak transcription	Stomach Smooth Muscle	stomach
38	chr1:84386800-84390000	Weak transcription	K562	blood
39	chr1:84386800-84392000	Weak transcription	Brain Anterior Caudate	brain
40	chr1:84386800-84398400	Weak transcription	HSMMtube	muscle
41	chr1:84386800-84398800	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr1:84386800-84403200	Weak transcription	NHDF-Ad	bronchial
43	chr1:84387000-84408400	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr1:84387000-84408400	Weak transcription	Fetal Muscle Leg	muscle
45	chr1:84387000-84410000	Weak transcription	Brain Germinal Matrix	brain
46	chr1:84388200-84391000	Weak transcription	Gastric	stomach
47	chr1:84388800-84402200	Weak transcription	HSMM	muscle
48	chr1:84389200-84390200	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr1:84389600-84391200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:84389800-84390600	Strong transcription	Fetal Brain Female	brain

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