Variant report

Variant	rs12029896
Chromosome Location	chr1:67163372-67163373
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10493414	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10889647	1.00[YRI][hapmap]
rs10889648	0.97[ASN][1000 genomes]
rs11208949	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11208950	0.96[ASN][1000 genomes]
rs12117649	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12563682	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1325265	0.98[ASN][1000 genomes]
rs1325266	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1359462	0.97[ASN][1000 genomes]
rs1359463	0.92[ASN][1000 genomes]
rs1408852	1.00[YRI][hapmap]
rs2031477	0.98[ASN][1000 genomes]
rs2146905	0.94[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap]
rs2454325	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.93[ASN][1000 genomes]
rs4143025	0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs475762	0.93[CEU][hapmap];0.89[CHB][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs510771	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs531378	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs566057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs587125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs609707	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs665379	0.93[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6668681	0.97[ASN][1000 genomes]
rs6682534	0.94[CHB][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs6686476	0.88[ASN][1000 genomes]
rs678499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7529763	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];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
rs12029896	LRRC7	cis	cerebellum	SCAN
rs12029896	PIN1L	cis	cerebellum	SCAN
rs12029896	TCTEX1D1	cis	multi-tissue	Pritchard
rs12029896	SGIP1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67155600-67167400	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr1:67155800-67164600	Weak transcription	Fetal Brain Male	brain
3	chr1:67155800-67168200	Weak transcription	Fetal Heart	heart
4	chr1:67155800-67177200	Weak transcription	Brain Anterior Caudate	brain
5	chr1:67156000-67177200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr1:67156200-67164400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:67156800-67166800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr1:67156800-67167600	Weak transcription	Brain Substantia Nigra	brain
9	chr1:67156800-67191400	Weak transcription	Fetal Brain Female	brain
10	chr1:67157000-67208800	Weak transcription	Brain Germinal Matrix	brain
11	chr1:67157200-67189600	Weak transcription	Brain Hippocampus Middle	brain
12	chr1:67157400-67191600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:67157600-67169400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:67158200-67189400	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr1:67158400-67191400	Weak transcription	Left Ventricle	heart
16	chr1:67158600-67166600	Weak transcription	NH-A	brain
17	chr1:67158600-67189400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr1:67159800-67169600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:67160000-67169600	Weak transcription	NHDF-Ad	bronchial
20	chr1:67160200-67169600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:67160400-67189400	Weak transcription	Brain Angular Gyrus	brain
22	chr1:67161200-67164400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:67161200-67164600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:67161200-67164600	Weak transcription	Aorta	Aorta
25	chr1:67161200-67171200	Weak transcription	Fetal Intestine Small	intestine
26	chr1:67161400-67164600	Weak transcription	NHLF	lung
27	chr1:67162800-67164600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:67162800-67166000	Weak transcription	Fetal Intestine Large	intestine

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