Variant report

Variant	rs536410
Chromosome Location	chr1:67191084-67191085
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:67166132..67168879-chr1:67189803..67192452,2	K562	blood:

Extended variants
information (count: 96 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1032634	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1032635	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10749763	0.96[CEU][hapmap]
rs10749765	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs10789210	0.95[CEU][hapmap]
rs10789214	1.00[CEU][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs10789215	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs10889634	0.96[CEU][hapmap]
rs10889635	0.92[CEU][hapmap]
rs10889641	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs10889642	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs10889643	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs10889644	1.00[CEU][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs11810644	1.00[CHB][hapmap]
rs12070427	1.00[CHB][hapmap]
rs1280280	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1280310	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1280313	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1325261	0.95[CEU][hapmap]
rs1325263	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs1536115	0.96[CEU][hapmap]
rs1562217	0.96[CEU][hapmap]
rs1570815	0.86[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	0.84[CEU][hapmap]
rs2025595	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2031478	0.96[CEU][hapmap]
rs2146904	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]
rs2146905	0.84[MKK][hapmap]
rs2147777	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs2483704	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]
rs2483705	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2872078	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs2916	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs4143025	0.84[MKK][hapmap]
rs4655506	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs4655636	0.92[CEU][hapmap]
rs4655647	0.96[CEU][hapmap]
rs4655648	0.96[CEU][hapmap]
rs4655650	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs481681	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs485521	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs485543	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs492109	1.00[CHB][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs499263	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs502690	0.91[CEU][hapmap];1.00[CHB][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs515944	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs523132	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs523188	0.96[CEU][hapmap];1.00[CHB][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs523956	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs524114	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs532564	1.00[ASN][1000 genomes]
rs536527	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs539014	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs544258	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs602513	0.96[CEU][hapmap];1.00[CHB][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs603750	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs618093	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs628655	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6588207	0.96[CEU][hapmap]
rs6588215	1.00[CEU][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs659291	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs665319	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6656912	0.92[CEU][hapmap]
rs6659968	0.96[CEU][hapmap]
rs6668603	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6669023	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6670378	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs6680876	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs6680944	0.96[CEU][hapmap]
rs6681460	0.96[CEU][hapmap]
rs6689864	0.96[CEU][hapmap]
rs6696927	0.96[CEU][hapmap]
rs6697088	0.96[CEU][hapmap]
rs672230	1.00[CHB][hapmap]
rs688630	1.00[ASN][1000 genomes]
rs693272	0.80[AMR][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	1.00[CEU][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs7521111	0.91[CEU][hapmap]
rs7521123	0.96[CEU][hapmap]
rs7524818	0.96[CEU][hapmap]
rs7542924	1.00[CEU][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs7554101	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9662943	0.96[CEU][hapmap]
rs9662962	0.95[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	esv997677	chr1:67186675-67194280	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs536410	TCTEX1D1	cis	cerebellum	SCAN
rs536410	SGIP1	cis	cerebellum	SCAN
rs536410	TCTEX1D1	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67156800-67191400	Weak transcription	Fetal Brain Female	brain
2	chr1:67157000-67208800	Weak transcription	Brain Germinal Matrix	brain
3	chr1:67157400-67191600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:67158400-67191400	Weak transcription	Left Ventricle	heart
5	chr1:67165200-67191400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:67165400-67191600	Weak transcription	Aorta	Aorta
7	chr1:67165400-67206800	Weak transcription	Fetal Brain Male	brain
8	chr1:67171400-67198000	Weak transcription	NHLF	lung
9	chr1:67179600-67191400	Weak transcription	NHDF-Ad	bronchial
10	chr1:67181200-67191200	Weak transcription	Brain Substantia Nigra	brain
11	chr1:67184800-67199400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr1:67185400-67191200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr1:67186400-67205000	Weak transcription	Fetal Heart	heart
14	chr1:67188200-67191200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:67188400-67191400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:67188600-67191400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr1:67188600-67217400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr1:67189400-67192200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:67189600-67192200	Enhancers	Brain Hippocampus Middle	brain
20	chr1:67190000-67191600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr1:67190000-67193800	Weak transcription	NH-A	brain
22	chr1:67190200-67201200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:67190400-67191400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:67190400-67191400	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr1:67190400-67191600	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr1:67190600-67191400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:67190600-67193600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:67190600-67195000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:67190800-67191200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr1:67190800-67191200	Weak transcription	Brain Angular Gyrus	brain
31	chr1:67190800-67191200	Weak transcription	Osteobl	bone
32	chr1:67190800-67191400	Weak transcription	Brain Anterior Caudate	brain
33	chr1:67191000-67192200	Enhancers	Liver	Liver

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