Variant report

Variant	rs12892792
Chromosome Location	chr14:24934910-24934911
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10130676	0.89[EUR][1000 genomes]
rs10135479	0.89[EUR][1000 genomes]
rs11622189	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap];0.81[LWK][hapmap];0.93[MEX][hapmap];0.88[MKK][hapmap];0.87[TSI][hapmap];0.81[YRI][hapmap]
rs11623993	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11848085	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12587663	0.89[EUR][1000 genomes]
rs12589069	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12589236	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12590069	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12590140	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12884912	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12886471	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12886673	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.81[LWK][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];0.86[TSI][hapmap];0.86[YRI][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12888681	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12889056	0.87[EUR][1000 genomes]
rs12889227	0.85[EUR][1000 genomes]
rs12889393	0.88[EUR][1000 genomes]
rs12890047	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12890665	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12891130	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12893160	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12893813	0.88[EUR][1000 genomes]
rs12894398	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12894530	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12896086	1.00[CEU][hapmap];0.87[JPT][hapmap];0.81[YRI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12896093	1.00[CEU][hapmap];0.87[JPT][hapmap];0.81[YRI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17200068	0.89[EUR][1000 genomes]
rs1951141	0.89[EUR][1000 genomes]
rs1956917	1.00[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap]
rs1956918	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs28656464	0.86[ASN][1000 genomes]
rs35019432	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35263299	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4982928	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4982932	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4982937	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56058252	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67775272	0.89[EUR][1000 genomes]
rs8005035	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8014706	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041336	chr14:24726564-25527319	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542000	chr14:24726564-25527319	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1053330	chr14:24908047-24993666	Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	n/a
4	nsv564061	chr14:24911138-24945331	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	n/a
5	esv2761824	chr14:24914008-24993666	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
6	nsv1043355	chr14:24914008-24993666	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
7	nsv1045732	chr14:24914008-25019317	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
8	esv19772	chr14:24914740-24951857	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
9	nsv523200	chr14:24915383-24975032	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
10	nsv521915	chr14:24915383-24992619	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
11	nsv564062	chr14:24915383-24992619	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
12	nsv1039955	chr14:24927313-24993666	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
13	nsv1035903	chr14:24929447-24981097	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
14	nsv542001	chr14:24929447-24981097	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
15	nsv1042290	chr14:24930993-24990765	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
16	nsv542002	chr14:24930993-24990765	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
17	esv18532	chr14:24932115-24947813	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12892792	METT11D1	cis	parietal	SCAN
rs12892792	TM9SF1	cis	cerebellum	SCAN
rs12892792	SDR39U1	cis	lymphoblastoid	seeQTL
rs12892792	IRF9	cis	parietal	SCAN
rs12892792	OR4K1	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:24912800-24950800	Weak transcription	Gastric	stomach
2	chr14:24922200-24946000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr14:24922800-24951000	Weak transcription	Pancreas	Pancrea
4	chr14:24923200-24937400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr14:24926000-24936000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr14:24927600-24951000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr14:24928200-24950400	Weak transcription	HepG2	liver
8	chr14:24928400-24936000	Weak transcription	Liver	Liver
9	chr14:24928600-24951000	Weak transcription	Placenta	Placenta
10	chr14:24928800-24951000	Weak transcription	Spleen	Spleen
11	chr14:24930800-24951000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr14:24932400-24936000	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr14:24932600-24935400	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr14:24932800-24935000	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr14:24932800-24935400	Enhancers	Thymus	Thymus
16	chr14:24932800-24935600	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr14:24932800-24935800	Enhancers	Primary T cells from cord blood	blood
18	chr14:24933000-24935200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr14:24933000-24935400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr14:24933000-24935600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr14:24933000-24951400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr14:24933200-24935600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr14:24934400-24935400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr14:24934400-24935400	Enhancers	Fetal Thymus	thymus

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