Variant report

Variant	rs2916
Chromosome Location	chr1:67216697-67216698
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1032634	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1032635	0.96[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10749763	0.84[CEU][hapmap]
rs10749765	0.87[CEU][hapmap]
rs10789210	0.81[CEU][hapmap]
rs10789214	0.88[CEU][hapmap]
rs10789215	0.88[CEU][hapmap]
rs10889634	0.84[CEU][hapmap]
rs10889635	0.80[CEU][hapmap]
rs10889641	0.82[CEU][hapmap]
rs10889642	0.88[CEU][hapmap]
rs10889643	0.88[CEU][hapmap]
rs10889644	0.88[CEU][hapmap]
rs11810644	1.00[CHB][hapmap]
rs12070427	1.00[CHB][hapmap]
rs1280280	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1280310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1280313	0.93[EUR][1000 genomes]
rs1325263	0.84[CEU][hapmap]
rs1536115	0.84[CEU][hapmap]
rs1562217	0.84[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	0.88[CEU][hapmap]
rs2025595	0.88[CEU][hapmap]
rs2031478	0.84[CEU][hapmap]
rs2146904	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs2147777	0.84[CEU][hapmap]
rs2483704	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]
rs2483705	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2872078	0.84[CEU][hapmap]
rs4655506	0.88[CEU][hapmap]
rs4655636	0.81[CEU][hapmap]
rs4655647	0.84[CEU][hapmap]
rs4655648	0.84[CEU][hapmap]
rs4655650	0.88[CEU][hapmap];0.81[MEX][hapmap]
rs481681	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs485521	0.82[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs485543	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs492109	1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs499263	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs502690	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs515944	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs523132	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs523188	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs523956	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs524114	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs532564	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs536410	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs536527	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs539014	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs544258	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs602513	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs603750	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs618093	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs628655	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6588207	0.84[CEU][hapmap]
rs6588215	0.88[CEU][hapmap]
rs659291	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs665319	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6656912	0.88[CEU][hapmap]
rs6659968	0.84[CEU][hapmap]
rs6668603	1.00[ASN][1000 genomes]
rs6670378	0.84[CEU][hapmap]
rs6680876	0.84[CEU][hapmap]
rs6680944	0.84[CEU][hapmap]
rs6681460	0.84[CEU][hapmap]
rs6689864	0.84[CEU][hapmap]
rs6696927	0.84[CEU][hapmap]
rs6697088	0.84[CEU][hapmap]
rs672230	1.00[CHB][hapmap];0.80[AMR][1000 genomes]
rs688630	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs693272	0.96[AMR][1000 genomes];0.98[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	0.88[CEU][hapmap]
rs7521123	0.83[CEU][hapmap]
rs7524818	0.84[CEU][hapmap]
rs7542924	0.88[CEU][hapmap]
rs7554101	0.84[CEU][hapmap];1.00[CHB][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs9662943	0.84[CEU][hapmap]
rs9662962	0.82[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
rs2916	TCTEX1D1	cis	parietal	SCAN
rs2916	TCTEX1D1	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67188600-67217400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr1:67192000-67217200	Weak transcription	Brain Angular Gyrus	brain
3	chr1:67192000-67217400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr1:67197000-67217600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:67205400-67217600	Weak transcription	Brain Hippocampus Middle	brain
6	chr1:67205600-67217600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:67205800-67217000	Weak transcription	NHLF	lung
8	chr1:67205800-67217400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr1:67205800-67217600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:67205800-67217800	Weak transcription	Aorta	Aorta
11	chr1:67207400-67217400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:67207400-67217400	Weak transcription	Brain Anterior Caudate	brain
13	chr1:67211600-67216800	Enhancers	Muscle Satellite Cultured Cells	--
14	chr1:67212800-67217600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:67213000-67217200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr1:67213200-67217600	Enhancers	HUVEC	blood vessel
17	chr1:67213600-67217600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:67213800-67217600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:67213800-67217600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:67214600-67217200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:67215200-67217200	Enhancers	Primary hematopoietic stem cells	blood
22	chr1:67215400-67217400	Enhancers	Primary T cells from cord blood	blood
23	chr1:67215600-67217200	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr1:67215600-67217600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:67215800-67217600	Weak transcription	NHDF-Ad	bronchial
26	chr1:67216000-67217400	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr1:67216000-67217600	Weak transcription	Osteobl	bone
28	chr1:67216400-67217000	Enhancers	Liver	Liver
29	chr1:67216400-67217200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:67216400-67217400	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr1:67216600-67217200	Weak transcription	Brain Germinal Matrix	brain

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