Variant report

Variant	rs12603115
Chromosome Location	chr17:46248994-46248995
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1002330	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10445339	0.83[EUR][1000 genomes]
rs10445377	0.81[EUR][1000 genomes]
rs10853098	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11079814	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11870056	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11872095	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12150533	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12452956	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12603380	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12941830	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12947089	0.92[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12952670	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1316657	0.92[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1452666	0.91[CEU][hapmap];0.81[CHB][hapmap]
rs1452667	0.91[CEU][hapmap];0.81[CHB][hapmap]
rs17620033	0.92[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs17681336	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1860862	0.92[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1860863	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2021752	0.92[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2021811	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2041572	0.92[CEU][hapmap];0.81[CHB][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2060876	0.91[CEU][hapmap];0.81[CHB][hapmap]
rs2072441	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2109982	0.92[CEU][hapmap];0.81[CHB][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2123341	0.92[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2278868	0.92[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2305433	0.92[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2924257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34949267	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3792692	0.92[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3792694	0.92[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3805363	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3805370	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3805371	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3897986	0.92[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3944039	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4793779	0.92[CEU][hapmap];0.85[CHB][hapmap]
rs4794447	0.85[CHB][hapmap]
rs4794505	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4794517	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4794525	0.82[EUR][1000 genomes]
rs55982346	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62064954	0.85[EUR][1000 genomes]
rs62066447	0.84[EUR][1000 genomes]
rs6504108	0.81[CHB][hapmap];0.83[CHD][hapmap]
rs7210149	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7213876	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7219967	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7220768	0.87[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7220922	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7223867	0.92[CEU][hapmap];0.80[CHB][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7225435	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7225550	0.92[CEU][hapmap];0.81[CHB][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7225865	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7501770	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs758999	0.92[CEU][hapmap];0.81[CHB][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8069064	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8069263	0.92[CEU][hapmap];0.81[CHB][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8071267	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8072282	0.92[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs8075270	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs882380	0.86[AMR][1000 genomes];0.84[EUR][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	nsv908576	chr17:46147807-46260366	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12603115	CBX1	cis	cerebellum	SCAN
rs12603115	NBR1	cis	parietal	SCAN
rs12603115	PRAC	cis	parietal	SCAN
rs12603115	SNX11	cis	parietal	SCAN
rs12603115	SNX11	cis	multi-tissue	Pritchard
rs12603115	SNX11	cis	Lymphoblastoid	GTEx
rs12603115	CDK5RAP3	cis	parietal	SCAN
rs12603115	HOXB2	cis	multi-tissue	Pritchard

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46216400-46251400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr17:46220800-46249000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr17:46236000-46250200	Strong transcription	Primary T cells fromperipheralblood	blood
4	chr17:46238200-46250800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr17:46239200-46253800	Weak transcription	Primary B cells from peripheral blood	blood
6	chr17:46240000-46250400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr17:46241000-46250200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr17:46241000-46253200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr17:46244800-46249200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr17:46245000-46252200	Weak transcription	GM12878-XiMat	blood
11	chr17:46245400-46250800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr17:46245800-46250600	Strong transcription	Primary T cells from cord blood	blood
13	chr17:46246200-46250200	Strong transcription	Primary T helper cells PMA-I stimulated	--
14	chr17:46246600-46250200	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr17:46247000-46250400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr17:46247000-46258600	Weak transcription	Primary B cells from cord blood	blood
17	chr17:46247400-46253000	Weak transcription	Thymus	Thymus
18	chr17:46247800-46250800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr17:46247800-46254400	Weak transcription	Fetal Thymus	thymus
20	chr17:46248000-46253000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr17:46248200-46253000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr17:46248400-46250400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr17:46248400-46250600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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