Variant report

Variant	rs316618
Chromosome Location	chr15:41796498-41796499
allele	A/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: 29 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11070328	0.81[YRI][hapmap]
rs11635906	0.93[YRI][hapmap]
rs11854632	0.81[YRI][hapmap]
rs11858812	0.81[YRI][hapmap]
rs12440111	0.86[AFR][1000 genomes]
rs13313520	0.81[YRI][hapmap]
rs13380007	0.81[YRI][hapmap]
rs1617832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs170296	1.00[JPT][hapmap]
rs1757457	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]
rs1757459	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]
rs1757460	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1757468	0.81[YRI][hapmap]
rs17730589	0.81[YRI][hapmap]
rs17730888	0.81[YRI][hapmap]
rs1899	0.81[YRI][hapmap]
rs2026945	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28463309	0.81[YRI][hapmap]
rs28578550	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316604	0.81[YRI][hapmap]
rs7164211	0.87[YRI][hapmap]
rs7165914	0.81[YRI][hapmap]
rs7169543	0.81[YRI][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
rs316618	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs316618	NDUFAF1	cis	Muscle Skeletal	GTEx
rs316618	OIP5-AS1	cis	Nerve Tibial	GTEx
rs316618	KRTAP4-7	cis	lesional skin	skin_eQTL
rs316618	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs316618	NDUFAF1	cis	multi-tissue	Pritchard
rs316618	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs316618	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs316618	LOC729082	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:27 , 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	chr15:41794800-41796600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
4	chr15:41794800-41796800	Strong transcription	Rectal Mucosa Donor 31	rectum
5	chr15:41795200-41799600	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr15:41795200-41800000	Weak transcription	Liver	Liver
7	chr15:41795400-41796600	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
8	chr15:41795400-41796600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr15:41795400-41796600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr15:41795400-41796600	Enhancers	Esophagus	oesophagus
11	chr15:41795400-41796800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr15:41795400-41800000	Weak transcription	Pancreas	Pancrea
13	chr15:41795400-41803600	Weak transcription	Lung	lung
14	chr15:41795400-41804200	Weak transcription	Right Atrium	heart
15	chr15:41795600-41799400	Weak transcription	Colonic Mucosa	Colon
16	chr15:41795600-41799400	Weak transcription	Gastric	stomach
17	chr15:41795600-41799400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr15:41795600-41801200	Strong transcription	Fetal Intestine Small	intestine
19	chr15:41795800-41796600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr15:41795800-41797600	Weak transcription	Spleen	Spleen
21	chr15:41796000-41796600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr15:41796000-41796800	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr15:41796000-41796800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr15:41796000-41796800	Enhancers	Stomach Mucosa	stomach
25	chr15:41796000-41797200	Strong transcription	Duodenum Mucosa	Duodenum
26	chr15:41796200-41797000	Strong transcription	Fetal Intestine Large	intestine
27	chr15:41796400-41800000	Weak transcription	HMEC	breast

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