Variant report

Variant	rs2146904
Chromosome Location	chr1:67160336-67160337
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1032634	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1032635	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10749763	0.92[CEU][hapmap]
rs10749765	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs10789210	0.90[CEU][hapmap]
rs10789214	0.96[CEU][hapmap];0.82[TSI][hapmap];0.89[EUR][1000 genomes]
rs10789215	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10889634	0.92[CEU][hapmap]
rs10889635	0.88[CEU][hapmap]
rs10889641	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs10889642	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs10889643	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs10889644	0.96[CEU][hapmap];0.82[TSI][hapmap];0.89[EUR][1000 genomes]
rs11810644	1.00[CHB][hapmap]
rs12070427	1.00[CHB][hapmap]
rs1280280	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1280310	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1280313	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1325261	0.90[CEU][hapmap]
rs1325263	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs1536115	0.92[CEU][hapmap]
rs1562217	0.92[CEU][hapmap]
rs1570815	0.88[EUR][1000 genomes]
rs17129327	1.00[CHB][hapmap]
rs17129329	1.00[CHB][hapmap]
rs17129365	1.00[CHB][hapmap]
rs17440989	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17492182	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1856318	0.80[CEU][hapmap]
rs2025595	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2031478	0.92[CEU][hapmap]
rs2147777	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs2483704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2483705	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2872078	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs2916	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs4655506	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs4655636	0.88[CEU][hapmap]
rs4655647	0.92[CEU][hapmap]
rs4655648	0.92[CEU][hapmap]
rs4655650	0.96[CEU][hapmap];0.83[MEX][hapmap];0.89[EUR][1000 genomes]
rs481681	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs485521	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs485543	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs492109	1.00[CHB][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs499263	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs502690	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs515944	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs523132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs523188	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs523956	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs524114	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs532564	1.00[ASN][1000 genomes]
rs536410	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs536527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs539014	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs544258	1.00[ASN][1000 genomes]
rs602513	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs603750	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap]
rs618093	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs628655	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6588207	0.92[CEU][hapmap]
rs6588215	0.96[CEU][hapmap];0.82[TSI][hapmap];0.89[EUR][1000 genomes]
rs659291	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs665319	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6656912	0.88[CEU][hapmap]
rs6659968	0.92[CEU][hapmap]
rs6668603	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6669023	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6670378	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs6680876	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs6680944	0.92[CEU][hapmap]
rs6681460	0.92[CEU][hapmap]
rs6689864	0.92[CEU][hapmap]
rs6696927	0.92[CEU][hapmap]
rs6697088	0.92[CEU][hapmap]
rs672230	1.00[CHB][hapmap]
rs688630	1.00[ASN][1000 genomes]
rs693272	1.00[ASN][1000 genomes]
rs72669501	1.00[ASN][1000 genomes]
rs72671621	1.00[ASN][1000 genomes]
rs72922021	1.00[ASN][1000 genomes]
rs7515848	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7519747	0.96[CEU][hapmap];0.82[TSI][hapmap];0.89[EUR][1000 genomes]
rs7521111	0.86[CEU][hapmap]
rs7521123	0.91[CEU][hapmap]
rs7524818	0.92[CEU][hapmap]
rs7542924	0.96[CEU][hapmap];0.82[TSI][hapmap];0.89[EUR][1000 genomes]
rs7554101	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9662943	0.92[CEU][hapmap]
rs9662962	0.91[CEU][hapmap]

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
rs2146904	TCTEX1D1	cis	cerebellum	SCAN
rs2146904	SGIP1	cis	cerebellum	SCAN
rs2146904	TCTEX1D1	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67140600-67161200	Weak transcription	Esophagus	oesophagus
2	chr1:67144600-67160800	Weak transcription	Lung	lung
3	chr1:67149200-67161000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr1:67152000-67162800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr1:67153400-67161200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:67155600-67167400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr1:67155800-67164600	Weak transcription	Fetal Brain Male	brain
8	chr1:67155800-67168200	Weak transcription	Fetal Heart	heart
9	chr1:67155800-67177200	Weak transcription	Brain Anterior Caudate	brain
10	chr1:67156000-67161400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:67156000-67177200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr1:67156200-67164400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:67156800-67166800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr1:67156800-67167600	Weak transcription	Brain Substantia Nigra	brain
15	chr1:67156800-67191400	Weak transcription	Fetal Brain Female	brain
16	chr1:67157000-67160800	Weak transcription	Aorta	Aorta
17	chr1:67157000-67208800	Weak transcription	Brain Germinal Matrix	brain
18	chr1:67157200-67160600	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr1:67157200-67160800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:67157200-67160800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr1:67157200-67189600	Weak transcription	Brain Hippocampus Middle	brain
22	chr1:67157400-67162200	Weak transcription	Fetal Intestine Large	intestine
23	chr1:67157400-67191600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr1:67157600-67169400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:67158200-67189400	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr1:67158400-67160800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:67158400-67191400	Weak transcription	Left Ventricle	heart
28	chr1:67158600-67166600	Weak transcription	NH-A	brain
29	chr1:67158600-67189400	Weak transcription	Brain Cingulate Gyrus	brain
30	chr1:67159200-67160400	Strong transcription	Brain Angular Gyrus	brain
31	chr1:67159600-67161400	Strong transcription	NHLF	lung
32	chr1:67159800-67161000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr1:67159800-67169600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:67160000-67169600	Weak transcription	NHDF-Ad	bronchial
35	chr1:67160200-67161200	Enhancers	Fetal Intestine Small	intestine
36	chr1:67160200-67169600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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