Variant report

Variant	rs12031054
Chromosome Location	chr1:67106825-67106826
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:67104788..67107666-chr1:67181908..67183681,2	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1014778	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10789211	0.83[ASW][hapmap]
rs10889633	0.87[JPT][hapmap]
rs10889639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11208930	0.85[YRI][hapmap]
rs11208934	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11208939	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11208944	0.86[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.83[TSI][hapmap]
rs11208945	0.86[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.83[TSI][hapmap]
rs1160675	0.87[JPT][hapmap]
rs11811699	0.85[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap]
rs12128857	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12402709	0.85[CEU][hapmap];0.85[JPT][hapmap]
rs12760606	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1359461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1408852	0.81[CEU][hapmap]
rs1445572	0.87[JPT][hapmap]
rs1838652	0.87[JPT][hapmap]
rs4143026	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs553729	0.81[CEU][hapmap]
rs55778510	0.99[ASN][1000 genomes]
rs650202	0.81[CEU][hapmap]
rs6588216	0.83[JPT][hapmap]
rs6656461	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6656705	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6656752	1.00[ASN][1000 genomes]
rs6666600	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6681164	0.93[ASN][1000 genomes]
rs6681263	0.97[ASN][1000 genomes]
rs6696973	0.87[JPT][hapmap]
rs6697365	0.87[JPT][hapmap]
rs7524680	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7526812	0.83[ASW][hapmap]
rs7537454	0.87[JPT][hapmap]
rs920987	0.87[JPT][hapmap]
rs963141	0.87[JPT][hapmap]
rs9659684	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9660797	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9662956	1.00[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	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12031054	TCTEX1D1	cis	multi-tissue	Pritchard
rs12031054	TCTEX1D1	cis	Whole Blood	GTEx
rs12031054	IL23R	cis	cerebellum	SCAN
rs12031054	SGIP1	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67088400-67114200	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr1:67090400-67155000	Weak transcription	Fetal Heart	heart
3	chr1:67090800-67108400	Weak transcription	Brain Anterior Caudate	brain
4	chr1:67091200-67107400	Weak transcription	NHDF-Ad	bronchial
5	chr1:67091200-67108600	Weak transcription	Osteobl	bone
6	chr1:67091200-67108800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr1:67091200-67128000	Weak transcription	NH-A	brain
8	chr1:67091400-67107400	Weak transcription	Fetal Brain Female	brain
9	chr1:67092000-67117200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:67092200-67114200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr1:67093200-67107800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:67096200-67108200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:67098800-67108800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:67099400-67115600	Weak transcription	Fetal Lung	lung
15	chr1:67100000-67144400	Weak transcription	Left Ventricle	heart
16	chr1:67100400-67108600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr1:67101000-67108800	Weak transcription	Brain Angular Gyrus	brain
18	chr1:67101200-67113600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:67101400-67110200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr1:67101600-67107400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:67101600-67110800	Weak transcription	Aorta	Aorta
22	chr1:67102600-67108800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:67102800-67120200	Weak transcription	Brain Germinal Matrix	brain
24	chr1:67103200-67107800	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr1:67103200-67112200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:67106200-67143000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr1:67106800-67107800	Weak transcription	NHLF	lung
28	chr1:67106800-67115800	Weak transcription	Fetal Brain Male	brain

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