Variant report

Variant	rs1617832
Chromosome Location	chr15:41789091-41789092
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:41784933-41789149	HepG2	liver:	n/a	n/a
2	POLR2A	chr15:41785067-41789397	HepG2	liver:	n/a	n/a
3	SUZ12	chr15:41786226-41789317	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:41767730..41772843-chr15:41782564..41789351,11	K562	blood:
2	chr15:41693279..41695491-chr15:41786361..41789615,3	K562	blood:
3	chr15:41784400..41789772-chr15:41847283..41854059,7	K562	blood:
4	chr15:41741913..41744692-chr15:41786667..41789132,2	K562	blood:
5	chr15:41787601..41789591-chr15:41827659..41829404,2	K562	blood:

No data

Variant related genes	Relation type
ITPKA	TF binding region
ENSG00000103932	Chromatin interaction
ENSG00000137806	Chromatin interaction
ENSG00000259838	Chromatin interaction
ENSG00000137815	Chromatin interaction
ENSG00000092445	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11070328	0.90[LWK][hapmap];0.81[YRI][hapmap]
rs11635906	0.93[YRI][hapmap]
rs11854081	0.81[YRI][hapmap]
rs11854632	0.90[LWK][hapmap];0.81[YRI][hapmap]
rs11858812	0.90[LWK][hapmap];0.81[YRI][hapmap]
rs12440111	0.85[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs13313520	0.90[LWK][hapmap];0.81[YRI][hapmap]
rs13380007	0.89[LWK][hapmap];0.81[YRI][hapmap]
rs170296	1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs1757457	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]
rs1757459	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]
rs1757460	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1757468	0.86[YRI][hapmap]
rs17730589	0.90[LWK][hapmap];0.81[YRI][hapmap]
rs17730888	0.81[YRI][hapmap]
rs1899	0.90[LWK][hapmap];0.81[YRI][hapmap]
rs2026945	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28463309	0.90[LWK][hapmap];0.81[YRI][hapmap]
rs28578550	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316604	0.85[LWK][hapmap];0.81[YRI][hapmap]
rs316618	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]
rs7164211	0.85[LWK][hapmap];0.87[YRI][hapmap]
rs7165914	0.81[YRI][hapmap]
rs7169543	0.90[LWK][hapmap];0.81[YRI][hapmap]
rs7181982	0.81[YRI][hapmap]
rs8036026	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:18)

SNP	Gene	Cis/trans	Tissue	Source
rs1617832	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs1617832	RPAP1	cis	parietal	SCAN
rs1617832	NUSAP1	cis	cerebellum	SCAN
rs1617832	NDUFAF1	cis	multi-tissue	Pritchard
rs1617832	FSIP1	cis	cerebellum	SCAN
rs1617832	OIP5-AS1	cis	Adipose Subcutaneous	GTEx
rs1617832	NUSAP1	cis	parietal	SCAN
rs1617832	OIP5-AS1	cis	Nerve Tibial	GTEx
rs1617832	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs1617832	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs1617832	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs1617832	GPR176	cis	parietal	SCAN
rs1617832	NDUFAF1	cis	cerebellum	SCAN
rs1617832	NDUFAF1	cis	lymphoblastoid	seeQTL
rs1617832	NDUFAF1	cis	Muscle Skeletal	GTEx
rs1617832	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs1617832	NDUFAF1	cis	parietal	SCAN
rs1617832	GPR176	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41785400-41789200	Active TSS	Brain Anterior Caudate	brain
2	chr15:41785400-41789400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
3	chr15:41788400-41789200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
4	chr15:41788600-41789200	Flanking Active TSS	Duodenum Mucosa	Duodenum
5	chr15:41788600-41789200	Flanking Active TSS	HepG2	liver
6	chr15:41788600-41789400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
7	chr15:41788600-41791000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr15:41788800-41789200	Weak transcription	Gastric	stomach
9	chr15:41788800-41789400	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
10	chr15:41788800-41790000	Enhancers	Stomach Mucosa	stomach
11	chr15:41788800-41790200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr15:41788800-41793400	Weak transcription	Pancreas	Pancrea
13	chr15:41788800-41793800	Weak transcription	Liver	Liver
14	chr15:41789000-41789200	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr15:41789000-41789200	Bivalent Enhancer	Small Intestine	intestine
16	chr15:41789000-41789400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr15:41789000-41789400	Flanking Active TSS	Fetal Intestine Large	intestine
18	chr15:41789000-41789400	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr15:41789000-41789400	Genic enhancers	K562	blood
20	chr15:41789000-41791000	Genic enhancers	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links