Variant report

Variant	rs2456045
Chromosome Location	chr15:76489917-76489918
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:76488936..76490866-chr15:76603480..76605348,2	MCF-7	breast:
2	chr15:76489752..76492594-chr15:76628754..76630476,2	K562	blood:
3	chr15:76484853..76487491-chr15:76488798..76492049,5	K562	blood:
4	chr15:76489835..76492594-chr15:76628976..76630921,2	K562	blood:
5	chr15:76487953..76490483-chr15:76500123..76503783,3	K562	blood:
6	chr15:76487373..76491413-chr15:76492592..76495149,4	K562	blood:
7	chr15:76488844..76490782-chr15:76625306..76628294,2	K562	blood:
8	chr15:76489717..76491571-chr15:76503812..76506764,2	K562	blood:
9	chr15:76486525..76491130-chr15:76491292..76495169,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000159556	Chromatin interaction
ENSG00000140374	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11072580	1.00[CEU][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11633749	0.87[ASN][1000 genomes]
rs12438741	0.91[EUR][1000 genomes]
rs12439484	0.96[CEU][hapmap];0.86[CHD][hapmap];0.80[JPT][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs12442266	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12592501	1.00[CEU][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12595211	1.00[CEU][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12595717	0.92[CEU][hapmap];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12595738	0.96[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12898415	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs12901160	0.88[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs12902506	0.92[CEU][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12907668	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs12907911	0.84[ASN][1000 genomes]
rs12908334	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12909718	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12910640	0.89[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs12911035	0.81[EUR][1000 genomes]
rs12913096	1.00[CEU][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.80[JPT][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs12916022	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1474117	1.00[CEU][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17361504	0.96[CEU][hapmap];0.81[CHD][hapmap];0.80[JPT][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs2139190	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2176623	1.00[CEU][hapmap];0.83[CHD][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs2456046	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]
rs2460154	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2469541	0.82[CEU][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2469542	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2469565	1.00[CEU][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2469566	0.96[CEU][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2959850	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2959853	1.00[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34213321	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34893715	0.81[EUR][1000 genomes]
rs35707798	0.84[EUR][1000 genomes]
rs3759853	1.00[CEU][hapmap];0.80[JPT][hapmap];0.83[EUR][1000 genomes]
rs3866543	0.84[CEU][hapmap];0.81[TSI][hapmap]
rs4381566	0.83[EUR][1000 genomes]
rs4886484	0.82[CEU][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs4886485	0.90[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7163036	0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs7174889	0.92[CEU][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs869452	1.00[CEU][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs959991	1.00[CEU][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.90[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2456045	ETFA	cis	cerebellum	SCAN
rs2456045	SCAPER	cis	cerebellum	SCAN
rs2456045	SCAPER	cis	lung	GTEx
rs2456045	NRG4	cis	parietal	SCAN
rs2456045	SCAPER	cis	parietal	SCAN

Chromatin state (count:104 , 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	chr15:76485400-76498400	Weak transcription	Fetal Brain Female	brain
7	chr15:76486000-76492000	Enhancers	Esophagus	oesophagus
8	chr15:76486800-76491800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr15:76486800-76503000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr15:76486800-76516600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr15:76487000-76492200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr15:76487000-76498200	Weak transcription	Primary T cells from cord blood	blood
13	chr15:76487400-76492400	Enhancers	Psoas Muscle	Psoas
14	chr15:76487600-76492000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr15:76487800-76490200	Enhancers	Right Atrium	heart
16	chr15:76487800-76492000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr15:76488000-76490600	Enhancers	Gastric	stomach
18	chr15:76488200-76490000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr15:76488200-76490000	Enhancers	Colon Smooth Muscle	Colon
20	chr15:76488200-76490200	Enhancers	Brain Hippocampus Middle	brain
21	chr15:76488200-76492000	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr15:76488200-76492200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr15:76488200-76492200	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr15:76488200-76492600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr15:76488400-76490000	Enhancers	HUVEC	blood vessel
26	chr15:76488400-76490000	Enhancers	NHDF-Ad	bronchial
27	chr15:76488400-76490200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr15:76488400-76490200	Enhancers	Brain Anterior Caudate	brain
29	chr15:76488400-76490200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr15:76488400-76490200	Enhancers	Rectal Smooth Muscle	rectum
31	chr15:76488400-76490200	Enhancers	Spleen	Spleen
32	chr15:76488400-76490400	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr15:76488400-76490400	Enhancers	Brain Substantia Nigra	brain
34	chr15:76488400-76490400	Enhancers	Duodenum Mucosa	Duodenum
35	chr15:76488400-76490400	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr15:76488400-76490600	Enhancers	Placenta	Placenta
37	chr15:76488400-76490800	Enhancers	Fetal Thymus	thymus
38	chr15:76488400-76490800	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr15:76488400-76490800	Flanking Active TSS	Hela-S3	cervix
40	chr15:76488400-76491200	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr15:76488400-76491200	Enhancers	HSMMtube	muscle
42	chr15:76488400-76491400	Enhancers	Colonic Mucosa	Colon
43	chr15:76488400-76491800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr15:76488400-76492000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr15:76488400-76492000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr15:76488400-76492200	Enhancers	Right Ventricle	heart
47	chr15:76488400-76492400	Enhancers	Left Ventricle	heart
48	chr15:76488400-76492400	Enhancers	NHLF	lung
49	chr15:76488400-76492600	Enhancers	HSMM	muscle
50	chr15:76488400-76492600	Enhancers	NH-A	brain

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