Variant report

Variant	rs1757463
Chromosome Location	chr15:41783814-41783815
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:41783805-41783845	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41783642..41785495-chr15:41786905..41788686,2	K562	blood:
2	chr15:41767730..41772843-chr15:41782564..41789351,11	K562	blood:

Variant related genes	Relation type
ITPKA	TF binding region
ENSG00000137815	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10518718	0.81[CHB][hapmap]
rs11631770	0.87[CHB][hapmap];0.87[LWK][hapmap]
rs13379756	0.87[CHB][hapmap]
rs1622914	0.97[ASN][1000 genomes]
rs1655557	0.95[ASN][1000 genomes]
rs16971767	0.87[CHB][hapmap]
rs16971798	0.87[CHB][hapmap]
rs16971806	0.81[CHB][hapmap]
rs1757456	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1757462	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2015781	0.87[CHB][hapmap]
rs2026946	0.97[ASN][1000 genomes]
rs2777491	0.87[CHB][hapmap];0.85[LWK][hapmap]
rs28526381	0.87[CHB][hapmap]
rs316605	0.87[CHB][hapmap];0.85[LWK][hapmap]
rs316609	0.87[CHB][hapmap]
rs316610	0.81[CHB][hapmap];0.87[LWK][hapmap]
rs316614	0.87[CHB][hapmap];0.84[LWK][hapmap]
rs316617	1.00[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs35826725	0.81[CHB][hapmap]
rs3743038	0.81[CHB][hapmap]
rs7163788	0.87[CHB][hapmap];0.85[LWK][hapmap]
rs7167498	0.81[CHB][hapmap]
rs7175800	0.81[CHB][hapmap]
rs7176588	0.81[CHB][hapmap]
rs7177641	0.87[CHB][hapmap];0.85[LWK][hapmap]
rs7178634	0.87[CHB][hapmap]
rs7178777	0.87[CHB][hapmap]
rs7180418	0.87[CHB][hapmap]
rs8024774	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs8026197	0.87[CHB][hapmap]
rs8032838	0.87[CHB][hapmap]
rs8036498	0.87[CHB][hapmap]
rs8041325	0.87[CHB][hapmap];0.85[LWK][hapmap]
rs823716	0.86[CHB][hapmap]
rs919961	0.87[CHB][hapmap]
rs9302109	0.87[CHB][hapmap]

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	nsv524476	chr15:41689232-41820200	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv904110	chr15:41776692-41813279	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv904111	chr15:41777898-41805115	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv471241	chr15:41783814-41820200	Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs1757463	NDUFAF1	cis	cerebellum	SCAN
rs1757463	NUSAP1	cis	parietal	SCAN
rs1757463	NDUFAF1	cis	lymphoblastoid	seeQTL
rs1757463	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs1757463	NDUFAF1	cis	multi-tissue	Pritchard
rs1757463	KRTAP4-7	cis	uninvolved skin	skin_eQTL
rs1757463	NDUFAF1	cis	parietal	SCAN
rs1757463	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs1757463	CASC5	cis	cerebellum	SCAN
rs1757463	RPAP1	cis	parietal	SCAN
rs1757463	OIP5-AS1	cis	Adipose Subcutaneous	GTEx
rs1757463	BMF	cis	parietal	SCAN
rs1757463	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs1757463	NDUFAF1	cis	Muscle Skeletal	GTEx
rs1757463	NUSAP1	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41773400-41785000	Weak transcription	A549	lung
2	chr15:41773800-41784000	Weak transcription	HepG2	liver
3	chr15:41774800-41784600	Weak transcription	Dnd41	blood
4	chr15:41775400-41784800	Weak transcription	Liver	Liver
5	chr15:41775600-41784800	Weak transcription	Brain Angular Gyrus	brain
6	chr15:41776000-41784400	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr15:41776000-41784800	Weak transcription	Brain Germinal Matrix	brain
8	chr15:41776800-41784200	Weak transcription	K562	blood
9	chr15:41776800-41784600	Weak transcription	Placenta	Placenta
10	chr15:41778600-41784800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr15:41779800-41785200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr15:41780400-41784000	Weak transcription	Right Ventricle	heart
13	chr15:41780400-41784600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr15:41780400-41784800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:41780600-41784600	Weak transcription	Right Atrium	heart
16	chr15:41780600-41784800	Weak transcription	Lung	lung
17	chr15:41781800-41785000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr15:41781800-41785000	Enhancers	NHDF-Ad	bronchial
19	chr15:41781800-41785200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr15:41782000-41784800	Enhancers	GM12878-XiMat	blood
21	chr15:41782000-41784800	Enhancers	Hela-S3	cervix
22	chr15:41782000-41784800	Enhancers	NHLF	lung
23	chr15:41782200-41784000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr15:41782200-41785000	Enhancers	HUVEC	blood vessel
25	chr15:41782200-41785200	Enhancers	NH-A	brain
26	chr15:41782400-41784400	Enhancers	NHEK	skin
27	chr15:41782400-41785000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr15:41782600-41784600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr15:41783400-41784600	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr15:41783400-41784800	Genic enhancers	Fetal Intestine Small	intestine
31	chr15:41783400-41785000	Enhancers	Spleen	Spleen
32	chr15:41783400-41785400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr15:41783600-41784000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr15:41783600-41784600	Weak transcription	HSMM	muscle
35	chr15:41783600-41784800	Enhancers	Duodenum Mucosa	Duodenum
36	chr15:41783600-41784800	Enhancers	Fetal Intestine Large	intestine
37	chr15:41783600-41785000	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr15:41783600-41785000	Enhancers	Stomach Mucosa	stomach
39	chr15:41783800-41784000	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr15:41783800-41784000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr15:41783800-41784000	Bivalent Enhancer	Primary T cells from cord blood	blood
42	chr15:41783800-41784000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
43	chr15:41783800-41784000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
44	chr15:41783800-41784000	Enhancers	Primary T killer memory cells from peripheral blood	blood
45	chr15:41783800-41784000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr15:41783800-41784000	Enhancers	Gastric	stomach
47	chr15:41783800-41784000	Enhancers	Placenta Amnion	Placenta Amnion
48	chr15:41783800-41784000	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
49	chr15:41783800-41784200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
50	chr15:41783800-41784800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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