Variant report

Variant	rs11208944
Chromosome Location	chr1:67143562-67143563
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1014778	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs10889639	0.83[CEU][hapmap];0.84[CHB][hapmap];0.84[JPT][hapmap]
rs10889647	0.90[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11208934	0.85[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap]
rs11208939	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs11208945	1.00[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];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11811699	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12031054	0.86[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.83[TSI][hapmap]
rs12043460	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12083409	0.93[ASW][hapmap]
rs12128857	0.85[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap]
rs12402709	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1280309	0.86[CEU][hapmap]
rs1359461	0.86[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap]
rs1408852	0.95[CEU][hapmap];0.81[CHD][hapmap];0.80[MEX][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16844	0.82[CHD][hapmap]
rs17129327	0.91[YRI][hapmap];0.82[AFR][1000 genomes]
rs35886191	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3738167	0.82[CHD][hapmap]
rs4143026	0.85[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap]
rs4655651	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs473470	0.91[CEU][hapmap]
rs487833	0.91[CEU][hapmap]
rs489300	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs512691	0.91[CEU][hapmap]
rs524204	0.91[CEU][hapmap]
rs553729	0.95[CEU][hapmap]
rs650202	0.95[CEU][hapmap];0.82[CHD][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs657808	0.91[CEU][hapmap]
rs6588216	0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6656461	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs6656705	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs6666600	0.85[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap]
rs678253	0.91[CEU][hapmap]
rs682896	0.82[CHD][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs693956	0.91[CEU][hapmap]
rs7512401	0.82[CHD][hapmap]
rs7524680	0.85[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap]
rs9659684	0.85[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap]
rs9660797	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs9988481	0.94[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11208944	SGIP1	cis	parietal	SCAN
rs11208944	TCTEX1D1	cis	Whole Blood	GTEx

Chromatin state (count:37 , 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	chr1:67109600-67155000	Weak transcription	Brain Anterior Caudate	brain
4	chr1:67111400-67154800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:67114200-67156400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr1:67121200-67145400	Weak transcription	Brain Angular Gyrus	brain
7	chr1:67135200-67154200	Weak transcription	Brain Hippocampus Middle	brain
8	chr1:67135600-67155400	Weak transcription	Brain Substantia Nigra	brain
9	chr1:67137400-67148000	Weak transcription	Fetal Brain Female	brain
10	chr1:67137600-67155000	Weak transcription	Brain Germinal Matrix	brain
11	chr1:67137800-67155000	Weak transcription	Fetal Brain Male	brain
12	chr1:67138000-67147200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr1:67138000-67154800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr1:67139200-67146400	Weak transcription	Fetal Lung	lung
15	chr1:67139600-67148000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr1:67139800-67145400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:67140400-67154800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:67140600-67161200	Weak transcription	Esophagus	oesophagus
19	chr1:67140800-67147400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:67141200-67148800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr1:67141600-67144800	Enhancers	NH-A	brain
22	chr1:67141800-67143600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr1:67141800-67144600	Enhancers	Muscle Satellite Cultured Cells	--
24	chr1:67141800-67144600	Enhancers	HUVEC	blood vessel
25	chr1:67142200-67145200	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr1:67142400-67144000	Enhancers	Osteobl	bone
27	chr1:67142400-67145200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:67142400-67148000	Weak transcription	Aorta	Aorta
29	chr1:67142600-67144600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:67142600-67144800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:67142600-67147200	Weak transcription	NHLF	lung
32	chr1:67142800-67147200	Weak transcription	NHDF-Ad	bronchial
33	chr1:67143000-67144800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:67143200-67143600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr1:67143400-67143800	Enhancers	HSMMtube	muscle
36	chr1:67143400-67145000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:67143400-67149800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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