Variant report

Variant	rs12913739
Chromosome Location	chr15:40882965-40882966
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ELF1	chr15:40882911-40883228	K562	blood:	n/a	n/a
2	GATA3	chr15:40882946-40883238	T-47D	breast:	n/a	n/a
3	IRF1	chr15:40882911-40883262	K562	blood:	n/a	n/a
4	GTF3C2	chr15:40881970-40883215	K562	blood:	n/a	n/a
5	MAX	chr15:40882729-40883094	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:40882574..40885236-chr15:41001374..41003078,2	K562	blood:
2	chr15:40876093..40878968-chr15:40880473..40883736,4	K562	blood:
3	chr15:40761695..40764555-chr15:40881844..40883742,2	K562	blood:
4	chr15:40867638..40870164-chr15:40881425..40883040,2	K562	blood:

No data

Variant related genes	Relation type
CASC5	TF binding region
ENSG00000169105	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 24 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10152546	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1044474	0.96[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs10518697	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1058734	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11070283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11630273	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11633184	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11637245	0.92[EUR][1000 genomes]
rs11637422	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12148915	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs12324748	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12385982	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12441754	0.85[EUR][1000 genomes]
rs12592524	0.93[CEU][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs12903817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12907442	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12908316	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12913296	0.93[EUR][1000 genomes]
rs12915171	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12915636	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13329076	0.87[EUR][1000 genomes]
rs17673703	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs17674454	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17747423	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17747633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1801321	0.93[CEU][hapmap]
rs1814541	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1814542	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2412525	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28529389	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28634695	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28647196	0.84[EUR][1000 genomes]
rs28669075	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34739056	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34824658	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35127391	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35684277	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35842610	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4923880	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4924486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4924496	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs62019876	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62019879	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6492964	0.85[CEU][hapmap]
rs71471880	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7165509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7170288	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7175747	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7177265	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs7180135	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs8029530	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8036891	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8037180	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8038122	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8042386	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs957603	0.92[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs9920642	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9920676	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv832984	chr15:40794391-40998535	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	esv2758378	chr15:40832545-40995111	Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2760026	chr15:40832545-40995111	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:24)

SNP	Gene	Cis/trans	Tissue	Source
rs12913739	C15orf57	cis	Esophagus Mucosa	GTEx
rs12913739	C15orf57	cis	Adipose Subcutaneous	GTEx
rs12913739	C15orf57	cis	Heart Left Ventricle	GTEx
rs12913739	RAD51	Cis_1M	lymphoblastoid	RTeQTL
rs12913739	RAD51	cis	multi-tissue	Pritchard
rs12913739	C15orf57	cis	Esophagus Muscularis	GTEx
rs12913739	CCDC32	cis	multi-tissue	Pritchard
rs12913739	C15orf57	cis	Skin Sun Exposed Lower leg	GTEx
rs12913739	C15orf57	cis	Artery Aorta	GTEx
rs12913739	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx
rs12913739	RP11-111A22.1	cis	lung	GTEx
rs12913739	CCDC32	cis	lesional skin	skin_eQTL
rs12913739	CCDC32	cis	uninvolved skin	skin_eQTL
rs12913739	RP11-111A22.1	cis	Artery Aorta	GTEx
rs12913739	RP11-111A22.1	cis	Heart Left Ventricle	GTEx
rs12913739	RP11-111A22.1	cis	Stomach	GTEx
rs12913739	RP11-111A22.1	cis	Artery Tibial	GTEx
rs12913739	CCDC32	cis	normal skin	skin_eQTL
rs12913739	C15orf57	cis	Artery Tibial	GTEx
rs12913739	C15orf57	cis	Nerve Tibial	GTEx
rs12913739	C15orf57	cis	Stomach	GTEx
rs12913739	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs12913739	C15orf57	cis	lung	GTEx
rs12913739	C15orf57	cis	Muscle Skeletal	GTEx

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40867400-40883600	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr15:40881800-40883000	Active TSS	Osteobl	bone
3	chr15:40881800-40883200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr15:40881800-40883200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr15:40881800-40883200	Enhancers	Primary B cells from peripheral blood	blood
6	chr15:40882000-40883000	Active TSS	Fetal Kidney	kidney
7	chr15:40882000-40883200	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr15:40882000-40883200	Active TSS	Ovary	ovary
9	chr15:40882000-40886200	Weak transcription	Lung	lung
10	chr15:40882200-40883000	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr15:40882200-40883000	Active TSS	Adipose Nuclei	Adipose
12	chr15:40882200-40883000	Enhancers	Liver	Liver
13	chr15:40882200-40883000	Active TSS	Thymus	Thymus
14	chr15:40882200-40883000	Active TSS	NHEK	skin
15	chr15:40882200-40883200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr15:40882200-40883200	Active TSS	Aorta	Aorta
17	chr15:40882200-40883200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
18	chr15:40882200-40883400	Active TSS	Fetal Stomach	stomach
19	chr15:40882200-40883400	Active TSS	Rectal Mucosa Donor 29	rectum
20	chr15:40882200-40883400	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr15:40882200-40883400	Active TSS	Right Atrium	heart
22	chr15:40882200-40883600	Active TSS	Fetal Intestine Large	intestine
23	chr15:40882200-40883800	Active TSS	HepG2	liver
24	chr15:40882200-40884000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr15:40882400-40883000	Flanking Active TSS	Fetal Intestine Small	intestine
26	chr15:40882400-40883000	Flanking Active TSS	Placenta	Placenta
27	chr15:40882400-40883400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr15:40882400-40883600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr15:40882400-40883600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr15:40882400-40883600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr15:40882400-40883800	Enhancers	Stomach Mucosa	stomach
32	chr15:40882400-40885000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr15:40882400-40886000	Weak transcription	Brain Substantia Nigra	brain
34	chr15:40882400-40886200	Weak transcription	HMEC	breast
35	chr15:40882600-40883000	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr15:40882600-40883000	Enhancers	Primary T cells fromperipheralblood	blood
37	chr15:40882600-40883000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr15:40882600-40883000	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr15:40882600-40883000	Enhancers	Fetal Muscle Trunk	muscle
40	chr15:40882600-40883000	Enhancers	Fetal Muscle Leg	muscle
41	chr15:40882600-40883000	Active TSS	Fetal Thymus	thymus
42	chr15:40882600-40883000	Enhancers	GM12878-XiMat	blood
43	chr15:40882600-40883000	Flanking Active TSS	HUVEC	blood vessel
44	chr15:40882600-40883000	Weak transcription	NHLF	lung
45	chr15:40882600-40883200	Flanking Active TSS	K562	blood
46	chr15:40882600-40883400	Enhancers	Primary B cells from cord blood	blood
47	chr15:40882600-40883400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr15:40882600-40883400	Weak transcription	A549	lung
49	chr15:40882600-40883600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr15:40882600-40883600	Enhancers	HUES6 Cell Line	embryonic stem cell

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