Variant report

Variant	rs2412657
Chromosome Location	chr15:42387203-42387204
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EBF1	chr15:42386840-42387204	GM12878	blood:	n/a	chr15:42386999-42387009 chr15:42386998-42387009
2	CTCF	chr15:42386710-42387212	MCF-7	breast:	n/a	chr15:42386954-42386967 chr15:42386900-42386908
3	CTCF	chr15:42386676-42387257	MCF-7	breast:	n/a	chr15:42386954-42386967 chr15:42386900-42386908
4	ZNF263	chr15:42386678-42387315	HEK293-T-REx	kidney:	n/a	chr15:42387083-42387092
5	RAD21	chr15:42386693-42387216	MCF-7	breast:	n/a	n/a
6	NFIC	chr15:42386635-42387334	ECC-1	luminal epithelium:	n/a	n/a
7	NFIC	chr15:42386585-42387297	ECC-1	luminal epithelium:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:42387193-42387243	HCF	heart:	n/a
2	chr15:42387193-42387243	Hela-S3	cervix:	n/a
3	chr15:42387193-42387243	HRPEpiC	eye:	n/a
4	chr15:42387193-42387243	SK-N-SH	brain:	n/a
5	chr15:42387193-42387243	NB4	blood:	n/a
6	chr15:42387193-42387243	NH-A	brain:	n/a
7	chr15:42387193-42387243	LNCaP	prostate:	n/a
8	chr15:42387193-42387243	Hepatocyte	liver:	n/a
9	chr15:42387193-42387243	IMR90	lung:	fetal
10	chr15:42387193-42387243	HUVEC	blood vessel:	n/a
11	chr15:42387193-42387243	SKMC	muscle:	n/a
12	chr15:42387193-42387243	HCM	heart:	n/a
13	chr15:42387193-42387243	HCPEpiC	choroid plexus:	n/a
14	chr15:42387193-42387243	ProgFib	skin:	n/a
15	chr15:42387193-42387243	K562	blood:	n/a
16	chr15:42387193-42387243	GM12878	blood:	n/a
17	chr15:42387193-42387243	HEK293	kidney:	embryo
18	chr15:42387193-42387243	H1-hESC	embryonic stem cell:	embryo
19	chr15:42387193-42387243	HIPEpiC	eye:	n/a
20	chr15:42387193-42387243	BE2_C	brain:	n/a
21	chr15:42387193-42387243	HCT-116	colon:	n/a
22	chr15:42387193-42387243	MCF10A-Er-Src	breast:	n/a
23	chr15:42387193-42387243	HPAEpiC	pulmonary alveolar:	n/a
24	chr15:42387193-42387243	GM12891	blood:	n/a
25	chr15:42387193-42387243	ECC-1	luminal epithelium:	n/a
26	chr15:42387193-42387243	AG04450	lung:	fetal
27	chr15:42387193-42387243	CMK	blood:	n/a
28	chr15:42387193-42387243	SK-N-MC	brain:	n/a
29	chr15:42387193-42387243	AoSMC	blood vessel:	n/a
30	chr15:42387193-42387243	AG10803	skin:	n/a
31	chr15:42387193-42387243	GM06990	blood:	n/a
32	chr15:42387193-42387243	HL-60	blood:	n/a
33	chr15:42387193-42387243	HNPCEpiC	eye:	n/a
34	chr15:42387193-42387243	GM12892	blood:	n/a
35	chr15:42387193-42387243	AG09309	skin:	n/a
36	chr15:42387193-42387243	T-47D	breast:	n/a
37	chr15:42387193-42387243	HEEpiC	esophagus:	n/a
38	chr15:42387193-42387243	Jurkat	blood:	n/a
39	chr15:42387193-42387243	U87	brain:	n/a
40	chr15:42387193-42387243	HRCEpiC	kidney:	n/a
41	chr15:42387193-42387243	NHDF-neo	bronchial:	n/a
42	chr15:42387193-42387243	HMEC	breast:	n/a
43	chr15:42387193-42387243	PFSK-1	brain:	n/a
44	chr15:42387193-42387243	HepG2	liver:	n/a
45	chr15:42387193-42387243	AG09319	gingival:	n/a
46	chr15:42387193-42387243	SAEC	small airway:	n/a
47	chr15:42387193-42387243	PrEC	prostate:	n/a
48	chr15:42387193-42387243	SK-N-SH_RA	brain:	n/a
49	chr15:42387193-42387243	NT2-D1	testis:	n/a
50	chr15:42387193-42387243	RPTEC	kidney:	n/a

No data

Variant related genes	Relation type
PLA2G4D	TF binding region
PLA2G4D	CpG island

Extended variants
information (count: 20 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10775125	0.85[ASN][1000 genomes]
rs11070359	0.81[CHB][hapmap];0.86[CHD][hapmap]
rs11629776	0.86[ASN][1000 genomes]
rs11632871	0.81[EUR][1000 genomes]
rs11635685	0.91[CHB][hapmap];0.86[CHD][hapmap];0.81[ASN][1000 genomes]
rs11638531	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs12902878	0.81[CHB][hapmap];0.81[CHD][hapmap]
rs1823551	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4924618	0.85[ASN][1000 genomes]
rs8031547	0.81[CHB][hapmap];0.88[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv1035998	chr15:42098896-42434254	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
3	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
6	nsv471683	chr15:42334375-42502982	Enhancers Bivalent Enhancer Genic enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv904131	chr15:42343794-42390223	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv904132	chr15:42343794-42398046	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv832985	chr15:42371482-42564966	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
10	nsv436201	chr15:42380264-42387429	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2412657	BAHD1	cis	cerebellum	SCAN
rs2412657	SPTBN5	cis	cerebellum	SCAN
rs2412657	CHAC1	cis	cerebellum	SCAN
rs2412657	ST3GAL5	trans	lymphoblastoid	seeQTL
rs2412657	IVD	cis	parietal	SCAN
rs2412657	TMEM62	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42384200-42387600	Enhancers	HMEC	breast
2	chr15:42384400-42388200	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr15:42385200-42387400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr15:42385400-42387400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr15:42385600-42392400	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr15:42385800-42387400	Enhancers	NHEK	skin
7	chr15:42386000-42387600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr15:42386000-42397600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr15:42386400-42387400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
10	chr15:42386600-42388400	Enhancers	Fetal Thymus	thymus
11	chr15:42386800-42388200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr15:42386800-42392200	Weak transcription	Gastric	stomach
13	chr15:42386800-42392600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr15:42386800-42392600	Weak transcription	Pancreas	Pancrea
15	chr15:42387200-42388400	Bivalent Enhancer	HepG2	liver
16	chr15:42387200-42389200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr15:42387200-42392600	Weak transcription	Esophagus	oesophagus

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