Variant report

Variant	rs7541249
Chromosome Location	chr1:67212427-67212428
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1014778	0.83[CEU][hapmap]
rs10789216	0.83[CEU][hapmap]
rs10889649	0.84[CEU][hapmap];0.95[YRI][hapmap];0.87[AMR][1000 genomes]
rs11208934	0.83[CEU][hapmap]
rs11208939	0.83[CEU][hapmap]
rs11208948	0.87[CEU][hapmap];0.84[AMR][1000 genomes]
rs11208951	0.88[CEU][hapmap];0.95[YRI][hapmap];0.87[AMR][1000 genomes]
rs11811067	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11811699	0.91[CEU][hapmap]
rs12119578	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12128857	0.83[CEU][hapmap]
rs12138266	0.87[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1280309	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1325268	0.83[CEU][hapmap];0.82[AMR][1000 genomes]
rs1498354	0.83[CEU][hapmap];0.87[AMR][1000 genomes]
rs1547644	1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs16844	0.83[CEU][hapmap];0.81[AMR][1000 genomes]
rs2016093	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2181625	0.83[CEU][hapmap];0.95[YRI][hapmap];0.87[AMR][1000 genomes]
rs2274987	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2312573	0.82[AMR][1000 genomes]
rs3738167	0.87[CEU][hapmap];0.86[AMR][1000 genomes]
rs4143026	0.83[CEU][hapmap]
rs473470	0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs485122	0.85[ASN][1000 genomes]
rs487833	0.86[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs500905	0.94[ASN][1000 genomes]
rs512691	0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs523544	0.89[ASN][1000 genomes]
rs524204	0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs531386	0.96[ASN][1000 genomes]
rs538659	0.89[ASN][1000 genomes]
rs553729	0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs562348	0.88[ASN][1000 genomes]
rs609906	0.83[ASN][1000 genomes]
rs609939	0.89[ASN][1000 genomes]
rs610295	0.88[ASN][1000 genomes]
rs624277	0.90[ASN][1000 genomes]
rs630410	0.95[ASN][1000 genomes]
rs657808	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6588216	0.91[CEU][hapmap]
rs6656461	0.83[CEU][hapmap]
rs6656705	0.83[CEU][hapmap]
rs6659325	0.84[CEU][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes]
rs6663604	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6666600	0.83[CEU][hapmap]
rs6679379	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs678253	0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs693956	0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs7512401	0.83[CEU][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes]
rs7524680	0.83[CEU][hapmap]
rs9659684	0.83[CEU][hapmap]
rs9660797	0.83[CEU][hapmap]
rs9988481	0.89[JPT][hapmap];0.85[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	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
2	nsv830093	chr1:67173594-67348264	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7541249	TCTEX1D1	cis	Whole Blood	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67188600-67217400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr1:67192000-67217200	Weak transcription	Brain Angular Gyrus	brain
3	chr1:67192000-67217400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr1:67196600-67212800	Weak transcription	Fetal Brain Female	brain
5	chr1:67197000-67217600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:67205400-67217600	Weak transcription	Brain Hippocampus Middle	brain
7	chr1:67205600-67217600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:67205800-67217000	Weak transcription	NHLF	lung
9	chr1:67205800-67217400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr1:67205800-67217600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:67205800-67217800	Weak transcription	Aorta	Aorta
12	chr1:67206000-67215600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr1:67207400-67217400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:67207400-67217400	Weak transcription	Brain Anterior Caudate	brain
15	chr1:67210400-67214000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:67211000-67212600	Enhancers	Primary hematopoietic stem cells	blood
17	chr1:67211600-67216800	Enhancers	Muscle Satellite Cultured Cells	--
18	chr1:67211800-67212600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:67211800-67213000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr1:67211800-67214800	Enhancers	NHDF-Ad	bronchial
21	chr1:67212000-67213600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:67212200-67212600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:67212200-67213800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:67212400-67212800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:67212400-67213800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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