Variant report

Variant	rs7540244
Chromosome Location	chr1:67136610-67136611
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10128053	0.94[CEU][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs10159265	0.82[EUR][1000 genomes]
rs10749764	0.90[ASN][1000 genomes]
rs11208911	1.00[CEU][hapmap]
rs11208922	0.86[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap]
rs11208940	1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs11208952	0.87[CEU][hapmap]
rs11208953	0.82[CEU][hapmap]
rs12062570	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs12069946	0.94[CEU][hapmap];0.81[JPT][hapmap]
rs12070270	0.94[CEU][hapmap];0.81[JPT][hapmap]
rs12072937	0.94[CEU][hapmap];0.81[JPT][hapmap]
rs12074963	0.94[CEU][hapmap];0.81[JPT][hapmap];0.90[TSI][hapmap]
rs12085282	0.94[CEU][hapmap]
rs12091471	0.94[CEU][hapmap];0.81[JPT][hapmap]
rs12091475	0.93[CEU][hapmap];0.81[JPT][hapmap]
rs12094526	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs13376692	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1530491	0.94[CEU][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs17129101	0.94[CEU][hapmap];0.96[GIH][hapmap];0.81[JPT][hapmap];0.95[TSI][hapmap]
rs17129226	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs17129244	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs17129245	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs17129252	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17129269	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17129307	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17440390	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs1832417	0.94[CEU][hapmap];0.87[GIH][hapmap];0.91[TSI][hapmap]
rs1988415	0.94[CEU][hapmap];0.87[GIH][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap]
rs20354	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap]
rs2166307	0.94[CEU][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs2182110	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3901541	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap]
rs41405244	0.94[CEU][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs41418445	0.94[CEU][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs41511845	0.94[CEU][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs4655642	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs5008753	1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap]
rs55817355	0.82[EUR][1000 genomes]
rs55895340	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs58418199	0.82[EUR][1000 genomes]
rs61313508	0.82[EUR][1000 genomes]
rs6588210	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap]
rs6588211	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs6588212	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap]
rs6588213	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs6664403	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6664597	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6664698	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap]
rs6670827	1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs6690186	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs6694782	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs72669463	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72669465	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72669469	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72669472	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72669475	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72669488	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74085003	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs74087510	0.82[EUR][1000 genomes]
rs7520353	0.94[CEU][hapmap];0.81[JPT][hapmap]
rs7528240	0.81[AMR][1000 genomes]
rs7531750	0.81[AMR][1000 genomes]
rs7536634	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7538967	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs7543378	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs7545674	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs7549727	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs920986	0.94[CEU][hapmap];0.90[JPT][hapmap]
rs9787219	0.88[CHB][hapmap];0.90[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	nsv869413	chr1:67082512-67414286	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7540244	SGIP1	cis	parietal	SCAN
rs7540244	TCTEX1D1	cis	parietal	SCAN
rs7540244	DLEU2L	cis	parietal	SCAN
rs7540244	TCTEX1D1	cis	cerebellum	SCAN
rs7540244	ANGPTL3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67090400-67155000	Weak transcription	Fetal Heart	heart
2	chr1:67100000-67144400	Weak transcription	Left Ventricle	heart
3	chr1:67106200-67143000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:67109200-67141800	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr1:67109600-67155000	Weak transcription	Brain Anterior Caudate	brain
6	chr1:67111400-67154800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:67114200-67142000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:67114200-67156400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr1:67114600-67142200	Weak transcription	NHLF	lung
10	chr1:67118800-67138800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:67118800-67140400	Weak transcription	Aorta	Aorta
12	chr1:67121200-67145400	Weak transcription	Brain Angular Gyrus	brain
13	chr1:67122000-67141200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:67131800-67141600	Weak transcription	NH-A	brain
15	chr1:67133200-67139200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr1:67133200-67141800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:67135000-67137200	Weak transcription	Brain Cingulate Gyrus	brain
18	chr1:67135000-67137800	Enhancers	Fetal Brain Male	brain
19	chr1:67135200-67154200	Weak transcription	Brain Hippocampus Middle	brain
20	chr1:67135600-67137200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr1:67135600-67155400	Weak transcription	Brain Substantia Nigra	brain
22	chr1:67135800-67141800	Weak transcription	NHDF-Ad	bronchial
23	chr1:67136000-67137000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:67136200-67137400	Enhancers	Fetal Brain Female	brain
25	chr1:67136400-67137400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:67136400-67137600	Enhancers	Primary B cells from cord blood	blood
27	chr1:67136600-67141600	Weak transcription	Osteobl	bone

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