Variant report

Variant	rs1757456
Chromosome Location	chr15:41793494-41793495
allele	A/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	JUND	chr15:41793415-41793566	HepG2	liver:	n/a	chr15:41793536-41793545 chr15:41793535-41793547 chr15:41793537-41793546 chr15:41793537-41793544 chr15:41793537-41793545
2	SIN3A	chr15:41793313-41793602	H1-hESC	embryonic stem cell:	n/a	chr15:41793481-41793490
3	JUND	chr15:41793416-41793610	H1-hESC	embryonic stem cell:	n/a	chr15:41793536-41793545 chr15:41793535-41793547 chr15:41793537-41793546 chr15:41793537-41793544 chr15:41793537-41793545
4	BACH1	chr15:41793416-41794057	H1-hESC	embryonic stem cell:	n/a	chr15:41793534-41793548
5	FOS	chr15:41793388-41793729	HUVEC	blood vessel:	n/a	chr15:41793535-41793546 chr15:41793536-41793545 chr15:41793535-41793547 chr15:41793537-41793546 chr15:41793537-41793544 chr15:41793537-41793545
6	JUND	chr15:41793370-41793722	H1-hESC	embryonic stem cell:	n/a	chr15:41793536-41793545 chr15:41793535-41793547 chr15:41793537-41793546 chr15:41793537-41793544 chr15:41793537-41793545
7	MXI1	chr15:41793094-41794115	IMR90	lung:	n/a	n/a
8	SUZ12	chr15:41793333-41795532	H1-hESC	embryonic stem cell:	n/a	n/a
9	RUNX3	chr15:41793455-41793718	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:41793472-41793522	SK-N-MC	brain:	n/a
2	chr15:41793472-41793522	AoSMC	blood vessel:	n/a
3	chr15:41793472-41793522	GM06990	blood:	n/a
4	chr15:41793472-41793522	NT2-D1	testis:	n/a
5	chr15:41793472-41793522	HL-60	blood:	n/a
6	chr15:41793472-41793522	AG04450	lung:	fetal
7	chr15:41793472-41793522	CMK	blood:	n/a
8	chr15:41793472-41793522	SKMC	muscle:	n/a
9	chr15:41793472-41793522	HEK293	kidney:	embryo
10	chr15:41793472-41793522	SK-N-SH	brain:	n/a
11	chr15:41793472-41793522	HMEC	breast:	n/a
12	chr15:41793472-41793522	PrEC	prostate:	n/a
13	chr15:41793472-41793522	HIPEpiC	eye:	n/a
14	chr15:41793472-41793522	GM12891	blood:	n/a
15	chr15:41793472-41793522	IMR90	lung:	fetal
16	chr15:41793472-41793522	HCF	heart:	n/a
17	chr15:41793472-41793522	MCF10A-Er-Src	breast:	n/a
18	chr15:41793472-41793522	Hela-S3	cervix:	n/a
19	chr15:41793472-41793522	Caco-2	colon:	n/a
20	chr15:41793472-41793522	MCF-7	breast:	n/a
21	chr15:41793472-41793522	U87	brain:	n/a
22	chr15:41793472-41793522	H1-hESC	embryonic stem cell:	embryo
23	chr15:41793472-41793522	PANC-1	pancreas:	n/a
24	chr15:41793472-41793522	BJ	skin:	n/a
25	chr15:41793472-41793522	NHDF-neo	bronchial:	n/a
26	chr15:41793472-41793522	HCT-116	colon:	n/a
27	chr15:41793472-41793522	LNCaP	prostate:	n/a
28	chr15:41793472-41793522	HRPEpiC	eye:	n/a
29	chr15:41793472-41793522	AG04449	skin:	fetal
30	chr15:41793472-41793522	HAEpiC	amniotic membrane:	n/a
31	chr15:41793472-41793522	HEEpiC	esophagus:	n/a
32	chr15:41793472-41793522	AG10803	skin:	n/a
33	chr15:41793472-41793522	Jurkat	blood:	n/a
34	chr15:41793472-41793522	NH-A	brain:	n/a
35	chr15:41793472-41793522	BE2_C	brain:	n/a
36	chr15:41793472-41793522	HCPEpiC	choroid plexus:	n/a
37	chr15:41793472-41793522	HCM	heart:	n/a
38	chr15:41793472-41793522	GM12878	blood:	n/a
39	chr15:41793472-41793522	HUVEC	blood vessel:	n/a
40	chr15:41793472-41793522	NB4	blood:	n/a
41	chr15:41793472-41793522	HepG2	liver:	n/a
42	chr15:41793472-41793522	HRE	kidney:	n/a
43	chr15:41793472-41793522	SAEC	small airway:	n/a
44	chr15:41793472-41793522	HNPCEpiC	eye:	n/a
45	chr15:41793472-41793522	ProgFib	skin:	n/a
46	chr15:41793472-41793522	SK-N-SH_RA	brain:	n/a
47	chr15:41793472-41793522	AG09319	gingival:	n/a
48	chr15:41793472-41793522	T-47D	breast:	n/a
49	chr15:41793472-41793522	Hepatocyte	liver:	n/a
50	chr15:41793472-41793522	AG09309	skin:	n/a

Variant related genes	Relation type
ITPKA	TF binding region
ITPKA	CpG island

Extended variants
information (count: 38 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11631770	0.84[CEU][hapmap];0.80[CHB][hapmap]
rs13379756	0.80[CHB][hapmap]
rs1622914	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1655557	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16971767	0.84[CEU][hapmap];0.80[CHB][hapmap]
rs16971798	0.84[CEU][hapmap];0.80[CHB][hapmap]
rs1757455	0.81[EUR][1000 genomes]
rs1757462	0.97[ASN][1000 genomes]
rs1757463	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2015781	0.85[CEU][hapmap];0.81[CHB][hapmap]
rs2026946	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2777491	0.84[CEU][hapmap];0.80[CHB][hapmap]
rs28526381	0.83[CEU][hapmap];0.80[CHB][hapmap]
rs316605	0.84[CEU][hapmap];0.80[CHB][hapmap];0.80[EUR][1000 genomes]
rs316609	0.90[CEU][hapmap];0.81[CHB][hapmap]
rs316610	0.84[CEU][hapmap]
rs316614	0.84[CEU][hapmap];0.80[CHB][hapmap]
rs316617	0.86[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3743038	0.84[CEU][hapmap]
rs7163788	0.84[CEU][hapmap];0.80[CHB][hapmap]
rs7177641	0.84[CEU][hapmap];0.80[CHB][hapmap]
rs7178634	0.84[CEU][hapmap];0.80[CHB][hapmap]
rs7178777	0.84[CEU][hapmap];0.80[CHB][hapmap]
rs7180418	0.84[CEU][hapmap];0.80[CHB][hapmap]
rs8024774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8026197	0.85[CEU][hapmap];0.81[CHB][hapmap]
rs8032838	0.84[CEU][hapmap];0.80[CHB][hapmap]
rs8036498	0.84[CEU][hapmap];0.80[CHB][hapmap]
rs8041325	0.84[CEU][hapmap];0.80[CHB][hapmap]
rs823716	0.86[CEU][hapmap]
rs919961	0.84[CEU][hapmap];0.80[CHB][hapmap]
rs9302109	0.84[CEU][hapmap];0.80[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	nsv569233	chr15:41784809-41805237	Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv33378	chr15:41786505-41805760	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1757456	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs1757456	NDUFAF1	cis	multi-tissue	Pritchard
rs1757456	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs1757456	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs1757456	NDUFAF1	cis	Muscle Skeletal	GTEx
rs1757456	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs1757456	KRTAP4-7	cis	uninvolved skin	skin_eQTL
rs1757456	OIP5-AS1	cis	Artery Tibial	GTEx
rs1757456	NDUFAF1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41788800-41793800	Weak transcription	Liver	Liver
2	chr15:41789400-41794000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr15:41789400-41794200	Weak transcription	Gastric	stomach
4	chr15:41789400-41802600	Weak transcription	K562	blood
5	chr15:41789600-41798200	Weak transcription	HepG2	liver
6	chr15:41792800-41793800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
7	chr15:41793200-41793600	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:41793200-41793600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr15:41793200-41793600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
10	chr15:41793200-41793600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
11	chr15:41793200-41793600	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
12	chr15:41793200-41793600	Bivalent Enhancer	Fetal Stomach	stomach
13	chr15:41793200-41793800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr15:41793200-41793800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
15	chr15:41793200-41793800	Bivalent Enhancer	Adipose Nuclei	Adipose
16	chr15:41793200-41793800	Bivalent Enhancer	Fetal Muscle Leg	muscle
17	chr15:41793200-41793800	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
18	chr15:41793200-41793800	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
19	chr15:41793200-41793800	Flanking Bivalent TSS/Enh	NH-A	brain
20	chr15:41793200-41794000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr15:41793200-41794000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
22	chr15:41793200-41794000	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
23	chr15:41793200-41794000	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
24	chr15:41793200-41794800	Bivalent Enhancer	Fetal Thymus	thymus
25	chr15:41793200-41795200	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
26	chr15:41793400-41793600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
27	chr15:41793400-41793600	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr15:41793400-41793600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
29	chr15:41793400-41793600	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
30	chr15:41793400-41793600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
31	chr15:41793400-41793600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
32	chr15:41793400-41793600	Flanking Bivalent TSS/Enh	Primary T helper naive cells from peripheral blood	blood
33	chr15:41793400-41793600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
34	chr15:41793400-41793600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
35	chr15:41793400-41793600	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
36	chr15:41793400-41793600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
37	chr15:41793400-41793600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr15:41793400-41793600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr15:41793400-41793600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
40	chr15:41793400-41793600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
41	chr15:41793400-41793600	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
42	chr15:41793400-41793600	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
43	chr15:41793400-41793600	Flanking Bivalent TSS/Enh	Thymus	Thymus
44	chr15:41793400-41793600	Bivalent Enhancer	NHDF-Ad	bronchial
45	chr15:41793400-41793800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
46	chr15:41793400-41793800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
47	chr15:41793400-41793800	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
48	chr15:41793400-41793800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr15:41793400-41793800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr15:41793400-41793800	Bivalent Enhancer	Brain Cingulate Gyrus	brain

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