Variant report

Variant	rs7312427
Chromosome Location	chr12:103834275-103834276
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10161218	0.92[GIH][hapmap]
rs10466955	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10467022	0.81[CHB][hapmap];0.91[GIH][hapmap]
rs10467023	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10745966	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]
rs10745969	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10778245	1.00[ASW][hapmap];0.88[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.96[TSI][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10860995	0.88[CEU][hapmap];0.94[GIH][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes]
rs10861006	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861012	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861023	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10861024	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10861027	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11111565	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1112754	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1316751	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1319091	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1320348	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2374049	0.91[GIH][hapmap]
rs2374063	0.88[EUR][1000 genomes]
rs2374067	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2374075	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2374076	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.87[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];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2888730	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs2888731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3953541	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4015523	0.94[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4015525	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4015527	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4015536	0.81[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4433658	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs4488299	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4506750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4764960	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6539076	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7295666	0.89[EUR][1000 genomes]
rs7295986	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs7296215	0.88[CEU][hapmap];0.97[GIH][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs7299547	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7301105	0.81[CHD][hapmap];0.92[GIH][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs7302598	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7307779	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7308343	0.88[CEU][hapmap];0.97[GIH][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs7316757	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7958520	0.94[CEU][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7959115	0.88[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs7960043	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7964462	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7969700	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7977907	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9669745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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	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
2	esv3338592	chr12:103817534-103849094	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7312427	TIMP3	trans	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:103824200-103834400	Weak transcription	Primary T cells from cord blood	blood
2	chr12:103828400-103834400	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr12:103828600-103834400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr12:103828800-103834400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr12:103829200-103834400	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr12:103832800-103834400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr12:103834200-103834400	Active TSS	Primary B cells from cord blood	blood
8	chr12:103834200-103834400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr12:103834200-103834400	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr12:103834200-103834400	Enhancers	Dnd41	blood
11	chr12:103834200-103834400	Active TSS	GM12878-XiMat	blood
12	chr12:103834200-103834800	Active TSS	Primary B cells from peripheral blood	blood

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