Variant report

Variant	rs2456046
Chromosome Location	chr15:76489113-76489114
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs11072576	0.88[CHB][hapmap]
rs11072579	0.86[CHB][hapmap]
rs11072580	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11072583	0.85[CHB][hapmap]
rs11072585	0.85[CHB][hapmap]
rs11072587	0.86[CHB][hapmap]
rs11634060	0.86[CHB][hapmap]
rs11636851	0.86[CHB][hapmap]
rs12050896	0.85[CHB][hapmap]
rs12438741	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12439484	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.80[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12442266	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12592501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12595211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12595717	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12595738	0.96[CEU][hapmap];0.88[JPT][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12898415	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12901160	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs12902506	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12907668	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12908334	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12909718	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12910640	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs12911035	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12913096	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.80[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12916022	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1474117	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16968083	0.86[CHB][hapmap]
rs17361504	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.80[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1850722	0.86[CHB][hapmap]
rs1875888	0.84[CHB][hapmap]
rs2139190	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2176623	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2456045	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2456050	0.86[CHB][hapmap]
rs2460154	0.92[CEU][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2469541	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2469542	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2469548	0.86[CHB][hapmap]
rs2469565	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2469566	0.96[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2959850	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.85[LWK][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2959853	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34213321	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34893715	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35707798	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3759853	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3784449	0.86[CHB][hapmap]
rs3866543	0.85[CEU][hapmap];0.85[TSI][hapmap]
rs3898352	0.86[CHB][hapmap]
rs4381566	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4886484	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs4886485	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs4886488	0.89[CHB][hapmap]
rs4886777	0.86[CHB][hapmap]
rs4886779	0.81[CHB][hapmap];0.81[ASN][1000 genomes]
rs4886783	0.86[CHB][hapmap]
rs4886787	0.86[CHB][hapmap]
rs4886788	0.86[CHB][hapmap]
rs4886789	0.86[CHB][hapmap]
rs4886791	0.86[CHB][hapmap]
rs7174889	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7177923	0.86[CHB][hapmap]
rs7180462	0.86[CHB][hapmap]
rs8028504	0.86[CHB][hapmap]
rs8029637	0.86[CHB][hapmap]
rs8030454	0.86[CHB][hapmap]
rs8033494	0.86[CHB][hapmap]
rs869452	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs870295	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs879625	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs883993	0.86[CHB][hapmap]
rs937732	0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs937733	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs959991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569998	chr15:76232605-76550938	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv1048760	chr15:76334544-76496977	Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv833057	chr15:76367848-76585868	ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv1036319	chr15:76432823-76489955	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
5	nsv1042750	chr15:76435640-76490547	ZNF genes & repeats Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
6	nsv1046099	chr15:76444695-76490547	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv1049916	chr15:76454194-76490547	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv1054713	chr15:76460462-76505906	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2456046	SCAPER	cis	Artery Tibial	GTEx
rs2456046	ETFA	cis	cerebellum	SCAN
rs2456046	NRG4	cis	parietal	SCAN
rs2456046	SCAPER	cis	lung	GTEx
rs2456046	ZNF291	cis	multi-tissue	Pritchard
rs2456046	SCAPER	cis	parietal	SCAN
rs2456046	SCAPER	cis	cerebellum	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76483600-76493400	Enhancers	Stomach Mucosa	stomach
2	chr15:76483800-76491800	Weak transcription	Liver	Liver
3	chr15:76484000-76498600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr15:76484000-76500800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr15:76484200-76498200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr15:76484600-76489200	Weak transcription	GM12878-XiMat	blood
7	chr15:76485400-76498400	Weak transcription	Fetal Brain Female	brain
8	chr15:76486000-76492000	Enhancers	Esophagus	oesophagus
9	chr15:76486400-76489200	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr15:76486800-76491800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr15:76486800-76503000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr15:76486800-76516600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr15:76487000-76492200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr15:76487000-76498200	Weak transcription	Primary T cells from cord blood	blood
15	chr15:76487400-76492400	Enhancers	Psoas Muscle	Psoas
16	chr15:76487600-76492000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr15:76487800-76489400	Flanking Active TSS	HepG2	liver
18	chr15:76487800-76489600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr15:76487800-76490200	Enhancers	Right Atrium	heart
20	chr15:76487800-76492000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr15:76488000-76489200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr15:76488000-76489600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
23	chr15:76488000-76489800	Enhancers	Fetal Muscle Trunk	muscle
24	chr15:76488000-76490600	Enhancers	Gastric	stomach
25	chr15:76488200-76489200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr15:76488200-76489400	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr15:76488200-76489800	Enhancers	Fetal Brain Male	brain
28	chr15:76488200-76490000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr15:76488200-76490000	Enhancers	Colon Smooth Muscle	Colon
30	chr15:76488200-76490200	Enhancers	Brain Hippocampus Middle	brain
31	chr15:76488200-76492000	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr15:76488200-76492200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr15:76488200-76492200	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr15:76488200-76492600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr15:76488400-76489200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr15:76488400-76489200	Enhancers	Aorta	Aorta
37	chr15:76488400-76489200	Enhancers	HMEC	breast
38	chr15:76488400-76489400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr15:76488400-76489600	Enhancers	Ovary	ovary
40	chr15:76488400-76489800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr15:76488400-76489800	Enhancers	Fetal Heart	heart
42	chr15:76488400-76489800	Enhancers	Fetal Intestine Small	intestine
43	chr15:76488400-76490000	Enhancers	HUVEC	blood vessel
44	chr15:76488400-76490000	Enhancers	NHDF-Ad	bronchial
45	chr15:76488400-76490200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr15:76488400-76490200	Enhancers	Brain Anterior Caudate	brain
47	chr15:76488400-76490200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr15:76488400-76490200	Enhancers	Rectal Smooth Muscle	rectum
49	chr15:76488400-76490200	Enhancers	Spleen	Spleen
50	chr15:76488400-76490400	Enhancers	Cortex derived primary cultured neurospheres	brain

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