Variant report

Variant	rs10745966
Chromosome Location	chr12:103817326-103817327
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10161218	0.88[CEU][hapmap];0.92[GIH][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs10466955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10467022	0.87[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap]
rs10467023	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10745969	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10778245	1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10860995	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10861006	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10861012	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10861023	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10861024	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10861027	0.86[EUR][1000 genomes]
rs11111565	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1112754	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1316751	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.87[YRI][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1319091	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs1320348	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2374049	0.91[GIH][hapmap];0.81[TSI][hapmap]
rs2374063	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2374067	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2374075	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2374076	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2374077	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2888730	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2888731	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3953541	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4015523	0.88[CEU][hapmap];0.93[EUR][1000 genomes]
rs4015525	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs4015527	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4015536	0.94[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4433658	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4488299	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4506750	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4764960	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6539076	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7295666	0.87[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7295986	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7296215	1.00[CEU][hapmap];0.97[GIH][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7299547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7301105	0.88[CEU][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs7302598	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7307779	0.84[EUR][1000 genomes]
rs7308343	1.00[CEU][hapmap];0.97[GIH][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.96[EUR][1000 genomes]
rs7312427	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.87[YRI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7316757	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7958520	0.94[CEU][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7959115	1.00[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.86[MEX][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7960043	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7964462	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7965797	0.86[EUR][1000 genomes]
rs7969700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7977907	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9669745	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv455703	chr12:103692799-103818049	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv560037	chr12:103692799-103818049	Enhancers Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv899477	chr12:103747515-103817326	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv899478	chr12:103747515-103834275	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10745966	TIMP3	trans	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:103812800-103828800	Weak transcription	Primary B cells from cord blood	blood
2	chr12:103815800-103818200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr12:103816000-103817400	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr12:103816000-103817400	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr12:103816000-103817400	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr12:103816000-103817600	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr12:103816000-103818000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr12:103816000-103818600	Enhancers	Fetal Brain Male	brain
9	chr12:103816200-103817600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr12:103816400-103819000	Strong transcription	Primary B cells from peripheral blood	blood
11	chr12:103816600-103817400	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:103816800-103818200	Enhancers	Brain Germinal Matrix	brain
13	chr12:103817200-103817600	Weak transcription	Fetal Brain Female	brain
14	chr12:103817200-103818800	Enhancers	Fetal Kidney	kidney
15	chr12:103817200-103819800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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