Variant report

Variant	rs10880696
Chromosome Location	chr12:45234989-45234990
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10506258	0.87[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs10785535	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs10785538	0.85[ASN][1000 genomes]
rs10785539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10880695	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11182706	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11615964	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12822444	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1376126	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs1506676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1506678	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1506679	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs2408084	0.87[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs2408085	0.83[CHB][hapmap]
rs374144	0.91[JPT][hapmap]
rs7295923	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7304472	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7305124	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7312377	0.83[ASN][1000 genomes]
rs7952764	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7953663	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7979717	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]

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	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	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
4	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
rs10880696	RP11-478B9.2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45213600-45237800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:45220600-45242000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr12:45221800-45242000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr12:45230000-45242200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:45230400-45236600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr12:45230800-45237400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr12:45231200-45237600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr12:45231200-45241600	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr12:45233600-45242000	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr12:45233800-45237200	Weak transcription	Fetal Brain Female	brain
11	chr12:45233800-45239800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr12:45234000-45235000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr12:45234000-45239800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr12:45234200-45235200	Weak transcription	Primary T cells from cord blood	blood
15	chr12:45234200-45235200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr12:45234400-45235400	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr12:45234400-45235800	Weak transcription	Fetal Brain Male	brain
18	chr12:45234800-45236000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:45234800-45242000	Enhancers	Primary T helper cells fromperipheralblood	blood

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