Variant report

Variant	rs316617
Chromosome Location	chr15:41795900-41795901
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:41794324..41796894-chr15:41811831..41813969,3	K562	blood:
2	chr15:41786611..41788959-chr15:41795033..41798597,3	MCF-7	breast:
3	chr15:41794716..41797159-chr15:41959395..41960897,2	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10518718	0.81[CHB][hapmap]
rs11631770	0.81[CEU][hapmap];0.87[CHB][hapmap];0.81[TSI][hapmap]
rs13379756	0.87[CHB][hapmap];0.84[TSI][hapmap]
rs1622914	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1655556	0.84[EUR][1000 genomes]
rs1655557	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16971767	0.81[CEU][hapmap];0.87[CHB][hapmap];0.86[TSI][hapmap]
rs16971798	0.81[CEU][hapmap];0.87[CHB][hapmap];0.86[TSI][hapmap]
rs16971806	0.81[CHB][hapmap]
rs1757455	0.83[EUR][1000 genomes]
rs1757456	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]
rs1757462	0.92[ASN][1000 genomes]
rs1757463	1.00[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs2015781	0.81[CEU][hapmap];0.87[CHB][hapmap]
rs2026946	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2777491	0.81[CEU][hapmap];0.87[CHB][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs28526381	0.80[CEU][hapmap];0.87[CHB][hapmap];0.86[TSI][hapmap]
rs316605	0.81[CEU][hapmap];0.87[CHB][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs316609	0.85[CEU][hapmap];0.87[CHB][hapmap];0.81[EUR][1000 genomes]
rs316610	0.81[CEU][hapmap];0.81[CHB][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs316613	0.80[EUR][1000 genomes]
rs316614	0.81[CEU][hapmap];0.87[CHB][hapmap];0.86[TSI][hapmap]
rs35826725	0.81[CHB][hapmap]
rs3743038	0.81[CEU][hapmap];0.81[CHB][hapmap];0.84[TSI][hapmap]
rs7163788	0.81[CEU][hapmap];0.87[CHB][hapmap];0.86[TSI][hapmap]
rs7167729	0.81[EUR][1000 genomes]
rs7175800	0.81[CHB][hapmap]
rs7177641	0.81[CEU][hapmap];0.87[CHB][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs7178634	0.81[CEU][hapmap];0.87[CHB][hapmap];0.86[TSI][hapmap]
rs7178777	0.81[CEU][hapmap];0.87[CHB][hapmap];0.86[TSI][hapmap]
rs7180418	0.81[CEU][hapmap];0.87[CHB][hapmap];0.86[TSI][hapmap]
rs8024774	0.86[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8026197	0.81[CEU][hapmap];0.87[CHB][hapmap]
rs8032838	0.81[CEU][hapmap];0.87[CHB][hapmap];0.86[TSI][hapmap]
rs8036498	0.81[CEU][hapmap];0.87[CHB][hapmap];0.86[TSI][hapmap]
rs8036527	0.84[EUR][1000 genomes]
rs8041325	0.81[CEU][hapmap];0.87[CHB][hapmap];0.86[TSI][hapmap]
rs823716	0.81[CEU][hapmap];0.86[CHB][hapmap];0.82[EUR][1000 genomes]
rs919961	0.81[CEU][hapmap];0.87[CHB][hapmap];0.84[TSI][hapmap]
rs9302109	0.81[CEU][hapmap];0.87[CHB][hapmap];0.86[TSI][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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs316617	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs316617	NDUFAF1	cis	lymphoblastoid	seeQTL
rs316617	NDUFAF1	cis	Muscle Skeletal	GTEx
rs316617	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs316617	OIP5-AS1	cis	Artery Tibial	GTEx
rs316617	NDUFAF1	cis	Esophagus Mucosa	GTEx
rs316617	KRTAP4-7	cis	uninvolved skin	skin_eQTL
rs316617	NDUFAF1	cis	multi-tissue	Pritchard
rs316617	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs316617	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs316617	LOC729082	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:46 , 50 per page) page: 1

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	chr15:41793800-41796200	ZNF genes & repeats	Fetal Intestine Large	intestine
4	chr15:41794400-41796000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
5	chr15:41794800-41796400	Enhancers	Brain Inferior Temporal Lobe	brain
6	chr15:41794800-41796600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
7	chr15:41794800-41796800	Strong transcription	Rectal Mucosa Donor 31	rectum
8	chr15:41795000-41796000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
9	chr15:41795000-41796000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
10	chr15:41795000-41796000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
11	chr15:41795000-41796000	Bivalent Enhancer	Fetal Thymus	thymus
12	chr15:41795200-41796000	Enhancers	Primary B cells from cord blood	blood
13	chr15:41795200-41796000	Bivalent Enhancer	Adipose Nuclei	Adipose
14	chr15:41795200-41796400	Bivalent Enhancer	NHEK	skin
15	chr15:41795200-41799600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr15:41795200-41800000	Weak transcription	Liver	Liver
17	chr15:41795400-41796000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr15:41795400-41796000	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
19	chr15:41795400-41796200	Bivalent Enhancer	Primary hematopoietic stem cells	blood
20	chr15:41795400-41796400	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr15:41795400-41796400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr15:41795400-41796400	Bivalent Enhancer	Fetal Brain Female	brain
23	chr15:41795400-41796400	Enhancers	HMEC	breast
24	chr15:41795400-41796600	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
25	chr15:41795400-41796600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr15:41795400-41796600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr15:41795400-41796600	Enhancers	Esophagus	oesophagus
28	chr15:41795400-41796800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr15:41795400-41800000	Weak transcription	Pancreas	Pancrea
30	chr15:41795400-41803600	Weak transcription	Lung	lung
31	chr15:41795400-41804200	Weak transcription	Right Atrium	heart
32	chr15:41795600-41796000	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
33	chr15:41795600-41796000	Weak transcription	Duodenum Mucosa	Duodenum
34	chr15:41795600-41796200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
35	chr15:41795600-41796200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr15:41795600-41799400	Weak transcription	Colonic Mucosa	Colon
37	chr15:41795600-41799400	Weak transcription	Gastric	stomach
38	chr15:41795600-41799400	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr15:41795600-41801200	Strong transcription	Fetal Intestine Small	intestine
40	chr15:41795800-41796000	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
41	chr15:41795800-41796000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
42	chr15:41795800-41796000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr15:41795800-41796000	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
44	chr15:41795800-41796400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
45	chr15:41795800-41796600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr15:41795800-41797600	Weak transcription	Spleen	Spleen

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