Variant report

Variant	rs2146905
Chromosome Location	chr1:67166893-67166894
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10493414	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10889648	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11208949	0.94[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.97[ASN][1000 genomes]
rs11208950	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12029896	0.94[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.97[ASN][1000 genomes]
rs12117649	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12563682	0.98[ASN][1000 genomes]
rs1325265	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1325266	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap]
rs1359462	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1359463	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2031477	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2454325	0.94[CHB][hapmap];0.87[JPT][hapmap];0.93[ASN][1000 genomes]
rs4143025	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.88[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs475762	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs510771	0.94[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.95[ASN][1000 genomes]
rs523132	0.81[ASW][hapmap];0.87[MKK][hapmap]
rs531378	0.95[ASN][1000 genomes]
rs536410	0.84[MKK][hapmap]
rs566057	0.94[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.95[ASN][1000 genomes]
rs587125	0.94[CHB][hapmap];0.88[JPT][hapmap];0.95[ASN][1000 genomes]
rs609707	0.94[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.95[ASN][1000 genomes]
rs665379	0.89[CHB][hapmap];0.83[ASN][1000 genomes]
rs6668681	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6682534	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6686476	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs678499	0.94[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs7529763	0.97[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2146905	SLC35D1	cis	parietal	SCAN
rs2146905	TCTEX1D1	cis	parietal	SCAN
rs2146905	TCTEX1D1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67155600-67167400	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr1:67155800-67168200	Weak transcription	Fetal Heart	heart
3	chr1:67155800-67177200	Weak transcription	Brain Anterior Caudate	brain
4	chr1:67156000-67177200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr1:67156800-67167600	Weak transcription	Brain Substantia Nigra	brain
6	chr1:67156800-67191400	Weak transcription	Fetal Brain Female	brain
7	chr1:67157000-67208800	Weak transcription	Brain Germinal Matrix	brain
8	chr1:67157200-67189600	Weak transcription	Brain Hippocampus Middle	brain
9	chr1:67157400-67191600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:67157600-67169400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:67158200-67189400	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr1:67158400-67191400	Weak transcription	Left Ventricle	heart
13	chr1:67158600-67189400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr1:67159800-67169600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:67160000-67169600	Weak transcription	NHDF-Ad	bronchial
16	chr1:67160200-67169600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:67160400-67189400	Weak transcription	Brain Angular Gyrus	brain
18	chr1:67161200-67171200	Weak transcription	Fetal Intestine Small	intestine
19	chr1:67164600-67168000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:67165200-67169800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:67165200-67170800	Weak transcription	NHLF	lung
22	chr1:67165200-67191400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:67165400-67187600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr1:67165400-67191600	Weak transcription	Aorta	Aorta
25	chr1:67165400-67206800	Weak transcription	Fetal Brain Male	brain
26	chr1:67166600-67170200	Weak transcription	Fetal Intestine Large	intestine
27	chr1:67166800-67169800	Weak transcription	Fetal Kidney	kidney

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