Variant report

Variant	rs2483704
Chromosome Location	chr1:67195353-67195354
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs1032634	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1032635	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10749763	0.92[CEU][hapmap]
rs10749765	0.96[CEU][hapmap]
rs10789210	0.90[CEU][hapmap]
rs10789214	0.96[CEU][hapmap]
rs10789215	0.96[CEU][hapmap]
rs10889634	0.92[CEU][hapmap]
rs10889635	0.88[CEU][hapmap]
rs10889641	0.91[CEU][hapmap]
rs10889642	0.96[CEU][hapmap]
rs10889643	0.96[CEU][hapmap]
rs10889644	0.96[CEU][hapmap]
rs11810644	1.00[CHB][hapmap]
rs12070427	1.00[CHB][hapmap]
rs1280280	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1280310	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1280313	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1325261	0.90[CEU][hapmap]
rs1325263	0.92[CEU][hapmap]
rs1536115	0.92[CEU][hapmap]
rs1562217	0.92[CEU][hapmap]
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]
rs2031478	0.92[CEU][hapmap]
rs2146904	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]
rs2147777	0.92[CEU][hapmap]
rs2483705	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2872078	0.92[CEU][hapmap]
rs2916	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4655506	0.96[CEU][hapmap]
rs4655636	0.88[CEU][hapmap]
rs4655647	0.92[CEU][hapmap]
rs4655648	0.92[CEU][hapmap]
rs4655650	0.96[CEU][hapmap]
rs481681	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs485521	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.84[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs485543	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs492109	1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs499263	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs502690	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs515944	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs523132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs523188	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs523956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs524114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.91[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];0.89[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs536527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs539014	0.92[CEU][hapmap];1.00[CHB][hapmap];0.80[MKK][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs544258	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs602513	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs603750	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs618093	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs628655	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6588207	0.92[CEU][hapmap]
rs6588215	0.96[CEU][hapmap]
rs659291	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs665319	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6656912	0.88[CEU][hapmap]
rs6659968	0.92[CEU][hapmap]
rs6668603	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6669023	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6670378	0.92[CEU][hapmap]
rs6680876	0.92[CEU][hapmap]
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	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];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]
rs7521111	0.86[CEU][hapmap]
rs7521123	0.91[CEU][hapmap]
rs7524818	0.92[CEU][hapmap]
rs7542924	0.96[CEU][hapmap]
rs7554101	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9662943	0.92[CEU][hapmap]
rs9662962	0.91[CEU][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2483704	TCTEX1D1	cis	cerebellum	SCAN
rs2483704	TCTEX1D1	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67157000-67208800	Weak transcription	Brain Germinal Matrix	brain
2	chr1:67165400-67206800	Weak transcription	Fetal Brain Male	brain
3	chr1:67171400-67198000	Weak transcription	NHLF	lung
4	chr1:67184800-67199400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr1:67186400-67205000	Weak transcription	Fetal Heart	heart
6	chr1:67188600-67217400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr1:67190200-67201200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:67191600-67195400	Enhancers	Muscle Satellite Cultured Cells	--
9	chr1:67191800-67196200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:67191800-67204600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:67191800-67204800	Weak transcription	Lung	lung
12	chr1:67192000-67195800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr1:67192000-67195800	Weak transcription	Fetal Brain Female	brain
14	chr1:67192000-67196200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:67192000-67197800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:67192000-67204600	Weak transcription	Aorta	Aorta
17	chr1:67192000-67204800	Weak transcription	Left Ventricle	heart
18	chr1:67192000-67217200	Weak transcription	Brain Angular Gyrus	brain
19	chr1:67192000-67217400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr1:67192200-67204600	Weak transcription	Brain Hippocampus Middle	brain
21	chr1:67192200-67208200	Weak transcription	Brain Substantia Nigra	brain
22	chr1:67192400-67204200	Weak transcription	Brain Anterior Caudate	brain
23	chr1:67193000-67195400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:67193000-67199600	Enhancers	Primary hematopoietic stem cells	blood
25	chr1:67193200-67197800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:67193400-67196000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:67193800-67195400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:67193800-67195400	Enhancers	NHEK	skin
29	chr1:67193800-67199600	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr1:67194000-67197400	Weak transcription	Osteobl	bone
31	chr1:67194200-67196800	Weak transcription	NHDF-Ad	bronchial
32	chr1:67194200-67198000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr1:67194200-67198200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr1:67194400-67195400	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr1:67194400-67195400	Flanking Active TSS	Dnd41	blood
36	chr1:67194600-67195400	Enhancers	Primary T cells from cord blood	blood
37	chr1:67194600-67195400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr1:67194800-67195400	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr1:67194800-67195600	Enhancers	Primary neutrophils fromperipheralblood	blood
40	chr1:67194800-67197800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr1:67195000-67195400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:67195000-67195400	Flanking Active TSS	HUVEC	blood vessel
43	chr1:67195000-67196200	Weak transcription	Thymus	Thymus
44	chr1:67195000-67196600	Enhancers	Fetal Thymus	thymus
45	chr1:67195200-67198000	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr1:67195200-67198000	Weak transcription	Monocytes-CD14+_RO01746	blood

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