Variant report

Variant	rs6696812
Chromosome Location	chr1:67100309-67100310
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10443224	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs10493410	0.87[JPT][hapmap]
rs11208909	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs11208915	0.91[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs11208920	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11208923	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs11208926	0.81[ASN][1000 genomes]
rs11208931	0.81[ASN][1000 genomes]
rs11208938	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11208941	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1159851	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs11799970	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs11806387	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs12032485	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12032691	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs12037314	0.91[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs12039010	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12040170	0.81[ASN][1000 genomes]
rs12041078	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs12044655	0.81[ASN][1000 genomes]
rs12045543	0.81[ASN][1000 genomes]
rs12048321	0.81[ASN][1000 genomes]
rs12049347	0.91[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs12116888	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs12120279	0.81[ASN][1000 genomes]
rs12125455	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs12126819	0.81[ASN][1000 genomes]
rs12127199	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12127884	0.81[ASN][1000 genomes]
rs12128429	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs12128496	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs12129319	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs12131306	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs12131909	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs12135689	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs12138066	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12139975	0.80[ASN][1000 genomes]
rs12725322	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs12726588	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12729740	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs12731043	0.81[ASN][1000 genomes]
rs12731104	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs12731112	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs12746750	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12751879	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs1373910	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs1536114	0.96[ASN][1000 genomes]
rs1570814	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs17129280	0.91[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs1900105	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs1925341	0.82[CHD][hapmap]
rs1975523	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs1998717	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1998718	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2121041	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs2312154	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2872079	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34007277	0.81[ASN][1000 genomes]
rs35156185	0.80[ASN][1000 genomes]
rs35902414	0.80[ASN][1000 genomes]
rs4233317	0.81[ASN][1000 genomes]
rs4428858	0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs4462119	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs4488004	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4655499	0.81[ASN][1000 genomes]
rs4655500	0.81[ASN][1000 genomes]
rs4655501	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs4655502	0.81[ASN][1000 genomes]
rs4655503	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs4655619	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs4655621	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs4655622	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs4655624	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs4655625	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs4655626	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs4655637	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs4655641	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs4655644	0.81[ASN][1000 genomes]
rs4655645	0.81[ASN][1000 genomes]
rs4655649	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6679568	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6680364	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7528182	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7546825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9787184	0.81[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
rs6696812	TCTEX1D1	cis	cerebellum	SCAN
rs6696812	DLEU2L	cis	parietal	SCAN
rs6696812	TCTEX1D1	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67088400-67114200	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr1:67090400-67155000	Weak transcription	Fetal Heart	heart
3	chr1:67090800-67108400	Weak transcription	Brain Anterior Caudate	brain
4	chr1:67091200-67100800	Weak transcription	Brain Angular Gyrus	brain
5	chr1:67091200-67100800	Weak transcription	NHLF	lung
6	chr1:67091200-67107400	Weak transcription	NHDF-Ad	bronchial
7	chr1:67091200-67108600	Weak transcription	Osteobl	bone
8	chr1:67091200-67108800	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr1:67091200-67128000	Weak transcription	NH-A	brain
10	chr1:67091400-67105200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr1:67091400-67107400	Weak transcription	Fetal Brain Female	brain
12	chr1:67092000-67117200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:67092200-67114200	Weak transcription	Primary hematopoietic stem cells	blood
14	chr1:67093200-67100800	Weak transcription	Aorta	Aorta
15	chr1:67093200-67107800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr1:67095200-67102000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:67096200-67100600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:67096200-67108200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr1:67098800-67108800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:67099000-67100400	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr1:67099000-67101000	Enhancers	Brain Hippocampus Middle	brain
22	chr1:67099400-67100800	Enhancers	Fetal Kidney	kidney
23	chr1:67099400-67115600	Weak transcription	Fetal Lung	lung
24	chr1:67099600-67100600	Enhancers	Brain Substantia Nigra	brain
25	chr1:67099800-67101600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr1:67100000-67101000	Weak transcription	Brain Cingulate Gyrus	brain
27	chr1:67100000-67144400	Weak transcription	Left Ventricle	heart
28	chr1:67100200-67100400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:67100200-67106200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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