Variant report

Variant	rs1757457
Chromosome Location	chr15:41794454-41794455
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41794324..41796894-chr15:41811831..41813969,3	K562	blood:

Extended variants
information (count: 19 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12440111	0.80[EUR][1000 genomes]
rs1617832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs170296	1.00[ASW][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes]
rs1757459	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1757460	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2026945	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2730056	1.00[LWK][hapmap]
rs28578550	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28631111	1.00[LWK][hapmap]
rs316611	1.00[LWK][hapmap]
rs316618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7164684	1.00[LWK][hapmap]
rs7168431	1.00[LWK][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:19)

SNP	Gene	Cis/trans	Tissue	Source
rs1757457	NUSAP1	cis	cerebellum	SCAN
rs1757457	NUSAP1	cis	parietal	SCAN
rs1757457	NDUFAF1	cis	lymphoblastoid	seeQTL
rs1757457	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs1757457	KRTAP4-7	cis	lesional skin	skin_eQTL
rs1757457	OIP5-AS1	cis	Nerve Tibial	GTEx
rs1757457	GPR176	cis	parietal	SCAN
rs1757457	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs1757457	NDUFAF1	cis	cerebellum	SCAN
rs1757457	FSIP1	cis	cerebellum	SCAN
rs1757457	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs1757457	GPR176	cis	cerebellum	SCAN
rs1757457	NDUFAF1	cis	Muscle Skeletal	GTEx
rs1757457	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs1757457	RPAP1	cis	parietal	SCAN
rs1757457	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs1757457	NDUFAF1	cis	multi-tissue	Pritchard
rs1757457	NDUFAF1	cis	parietal	SCAN
rs1757457	ITPKA	cis	multi-tissue	Pritchard

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41789400-41802600	Weak transcription	K562	blood
2	chr15:41789600-41798200	Weak transcription	HepG2	liver
3	chr15:41793200-41794800	Bivalent Enhancer	Fetal Thymus	thymus
4	chr15:41793200-41795200	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
5	chr15:41793400-41794600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
6	chr15:41793400-41794600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
7	chr15:41793400-41794800	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr15:41793400-41795000	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
9	chr15:41793400-41795200	Bivalent Enhancer	Fetal Heart	heart
10	chr15:41793400-41795200	Bivalent/Poised TSS	Psoas Muscle	Psoas
11	chr15:41793400-41795400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
12	chr15:41793400-41795400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
13	chr15:41793400-41795400	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr15:41793400-41795400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr15:41793400-41795400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr15:41793400-41795400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
17	chr15:41793400-41795400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr15:41793400-41795400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr15:41793400-41795400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr15:41793400-41795400	Enhancers	Pancreas	Pancrea
21	chr15:41793400-41795600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
22	chr15:41793400-41795600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
23	chr15:41793400-41795600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr15:41793400-41795600	Bivalent Enhancer	Fetal Brain Male	brain
25	chr15:41793400-41795600	ZNF genes & repeats	Fetal Intestine Small	intestine
26	chr15:41793400-41795800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr15:41793400-41795800	Enhancers	Spleen	Spleen
28	chr15:41793600-41794800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
29	chr15:41793600-41794800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
30	chr15:41793600-41795000	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
31	chr15:41793600-41795600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
32	chr15:41793800-41794600	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
33	chr15:41793800-41794800	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr15:41793800-41794800	Flanking Active TSS	Right Atrium	heart
35	chr15:41793800-41795000	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
36	chr15:41793800-41795000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
37	chr15:41793800-41795200	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
38	chr15:41793800-41795200	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
39	chr15:41793800-41795200	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
40	chr15:41793800-41795200	Enhancers	Liver	Liver
41	chr15:41793800-41795400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr15:41793800-41795400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr15:41793800-41795400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr15:41793800-41795600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
45	chr15:41793800-41795800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
46	chr15:41793800-41796200	ZNF genes & repeats	Fetal Intestine Large	intestine
47	chr15:41794000-41794800	Bivalent Enhancer	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr15:41794000-41794800	Bivalent Enhancer	Placenta	Placenta
49	chr15:41794000-41795000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
50	chr15:41794000-41795000	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood

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