Variant report

Variant	rs12657678
Chromosome Location	chr5:49860118-49860119
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10050458	0.96[ASN][1000 genomes]
rs10050633	0.96[ASN][1000 genomes]
rs1037194	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10454829	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10454830	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10940390	0.80[ASN][1000 genomes]
rs11741135	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12187591	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12659667	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13159524	0.95[ASN][1000 genomes]
rs1364023	0.98[ASN][1000 genomes]
rs1423646	0.87[ASN][1000 genomes]
rs1423647	0.80[ASN][1000 genomes]
rs1423648	0.98[ASN][1000 genomes]
rs1550981	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1833904	0.96[ASN][1000 genomes]
rs1963472	0.80[ASN][1000 genomes]
rs2042343	0.80[ASN][1000 genomes]
rs2354168	0.80[ASN][1000 genomes]
rs4605740	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4610419	0.96[ASN][1000 genomes]
rs4865844	0.96[ASN][1000 genomes]
rs4865847	0.96[ASN][1000 genomes]
rs4865855	0.96[ASN][1000 genomes]
rs6450183	0.94[ASN][1000 genomes]
rs6450219	0.96[ASN][1000 genomes]
rs6862802	0.96[ASN][1000 genomes]
rs7704183	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7721806	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7723800	0.80[ASN][1000 genomes]
rs7727359	0.96[ASN][1000 genomes]
rs7731983	0.96[ASN][1000 genomes]
rs9292065	0.80[ASN][1000 genomes]
rs962424	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032003	chr5:49455624-49881491	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1016583	chr5:49455624-50116720	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1023140	chr5:49455624-50121623	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1023981	chr5:49584188-49871537	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv537757	chr5:49584188-49871537	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1022067	chr5:49584188-49960083	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv537758	chr5:49584188-49960083	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv918220	chr5:49584188-50111282	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv931010	chr5:49584189-50118254	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv523212	chr5:49597497-50058043	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	esv2757995	chr5:49748352-50058182	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	esv2759342	chr5:49748352-50058182	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12657678	ZC3H12C	trans	parietal	SCAN
rs12657678	PARP8	Cis_1M	lymphoblastoid	RTeQTL
rs12657678	LOC647121	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49859400-49862400	Enhancers	Primary T helper cells fromperipheralblood	blood
2	chr5:49859400-49863200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr5:49859600-49860200	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr5:49859600-49860200	Enhancers	NHEK	skin
5	chr5:49859600-49860800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr5:49859600-49860800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
7	chr5:49859600-49860800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr5:49859600-49860800	Flanking Active TSS	Dnd41	blood
9	chr5:49859600-49860800	Enhancers	GM12878-XiMat	blood
10	chr5:49859600-49861000	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr5:49859600-49861200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr5:49859600-49861600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr5:49859600-49862600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr5:49859600-49862600	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr5:49859600-49862800	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr5:49859800-49860400	Enhancers	Primary hematopoietic stem cells	blood
17	chr5:49859800-49860800	Enhancers	Primary T cells from cord blood	blood
18	chr5:49859800-49860800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr5:49859800-49861200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr5:49860000-49860800	Enhancers	Primary T cells fromperipheralblood	blood
21	chr5:49860000-49860800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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