Variant report

Variant	rs10880666
Chromosome Location	chr12:45145920-45145921
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1037433	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10506256	0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10785515	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10880655	0.82[CEU][hapmap]
rs10880658	0.95[CHB][hapmap];0.85[JPT][hapmap];0.80[YRI][hapmap]
rs10880659	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs10880660	0.80[ASN][1000 genomes]
rs10880673	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11182559	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs11182596	0.80[ASN][1000 genomes]
rs11182634	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11182635	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11182636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11182640	0.84[CHB][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12303497	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12312100	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12815257	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1563043	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs1850406	0.81[CHD][hapmap]
rs1869162	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs2060840	0.92[CEU][hapmap];0.84[CHB][hapmap]
rs2060895	0.84[ASW][hapmap]
rs2060896	0.84[ASW][hapmap];0.80[YRI][hapmap]
rs2305448	0.91[ASW][hapmap];0.89[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs3858727	0.97[ASN][1000 genomes]
rs4544065	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4768066	0.89[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.80[YRI][hapmap]
rs4768564	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs583575	0.94[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs605722	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs615760	0.94[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs628408	0.95[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.90[MKK][hapmap];0.85[ASN][1000 genomes]
rs632481	0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs636843	0.94[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs6582509	0.84[ASW][hapmap]
rs678663	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs688669	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7299365	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs7301539	0.80[ASN][1000 genomes]
rs7308509	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7310844	0.80[ASN][1000 genomes]
rs7958608	0.84[ASW][hapmap]
rs7968076	0.81[YRI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs838973	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs966383	1.00[CHB][hapmap];0.90[JPT][hapmap];0.80[YRI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs978540	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3378050	chr12:44963059-45264289	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv832394	chr12:45077573-45269305	Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
3	nsv1049080	chr12:45097564-45195295	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
4	nsv1036926	chr12:45131884-45273648	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
5	nsv541484	chr12:45131884-45273648	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10880666	TMEM117	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45134400-45165200	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr12:45135400-45175000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:45145000-45146000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr12:45145000-45150200	Weak transcription	Fetal Brain Male	brain
5	chr12:45145000-45150600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:45145000-45172200	Weak transcription	Fetal Brain Female	brain
7	chr12:45145200-45169600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr12:45145400-45146400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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