Variant report

Variant	rs897466
Chromosome Location	chr15:93014483-93014484
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:93014270-93016473	H1-neurons	neurons:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:93014435-93014485	BE2_C	brain:	n/a
2	chr15:93014435-93014485	HUVEC	blood vessel:	n/a
3	chr15:93014435-93014485	AoSMC	blood vessel:	n/a
4	chr15:93014435-93014485	PFSK-1	brain:	n/a
5	chr15:93014435-93014485	RPTEC	kidney:	n/a
6	chr15:93014435-93014485	ECC-1	luminal epithelium:	n/a
7	chr15:93014435-93014485	HepG2	liver:	n/a
8	chr15:93014435-93014485	GM12892	blood:	n/a
9	chr15:93014435-93014485	ovcar-3	ovarian:	n/a
10	chr15:93014435-93014485	Caco-2	colon:	n/a
11	chr15:93014435-93014485	HRCEpiC	kidney:	n/a
12	chr15:93014435-93014485	NHBE	bronchial:	n/a
13	chr15:93014435-93014485	AG04450	lung:	fetal
14	chr15:93014435-93014485	ProgFib	skin:	n/a
15	chr15:93014435-93014485	HMEC	breast:	n/a
16	chr15:93014435-93014485	NB4	blood:	n/a
17	chr15:93014435-93014485	HIPEpiC	eye:	n/a
18	chr15:93014435-93014485	NH-A	brain:	n/a
19	chr15:93014435-93014485	IMR90	lung:	fetal
20	chr15:93014435-93014485	GM19239	blood:	n/a
21	chr15:93014435-93014485	AG10803	skin:	n/a
22	chr15:93014435-93014485	T-47D	breast:	n/a
23	chr15:93014435-93014485	BJ	skin:	n/a
24	chr15:93014435-93014485	NT2-D1	testis:	n/a
25	chr15:93014435-93014485	HL-60	blood:	n/a
26	chr15:93014435-93014485	GM12878	blood:	n/a
27	chr15:93014435-93014485	SK-N-MC	brain:	n/a
28	chr15:93014435-93014485	HCF	heart:	n/a
29	chr15:93014435-93014485	CMK	blood:	n/a
30	chr15:93014435-93014485	MCF10A-Er-Src	breast:	n/a
31	chr15:93014435-93014485	AG09309	skin:	n/a
32	chr15:93014435-93014485	AG04449	skin:	fetal
33	chr15:93014435-93014485	HRE	kidney:	n/a
34	chr15:93014435-93014485	AG09319	gingival:	n/a
35	chr15:93014435-93014485	LNCaP	prostate:	n/a
36	chr15:93014435-93014485	GM06990	blood:	n/a
37	chr15:93014435-93014485	HNPCEpiC	eye:	n/a
38	chr15:93014435-93014485	H1-hESC	embryonic stem cell:	embryo
39	chr15:93014435-93014485	HEEpiC	esophagus:	n/a
40	chr15:93014435-93014485	HCM	heart:	n/a
41	chr15:93014435-93014485	A549	lung:	n/a
42	chr15:93014435-93014485	SK-N-SH_RA	brain:	n/a
43	chr15:93014435-93014485	U87	brain:	n/a
44	chr15:93014435-93014485	HRPEpiC	eye:	n/a
45	chr15:93014435-93014485	NHDF-neo	bronchial:	n/a
46	chr15:93014435-93014485	PrEC	prostate:	n/a
47	chr15:93014435-93014485	K562	blood:	n/a
48	chr15:93014435-93014485	MCF-7	breast:	n/a
49	chr15:93014435-93014485	HEK293	kidney:	embryo
50	chr15:93014435-93014485	SAEC	small airway:	n/a

No data

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM174B-3	chr15:93014471-93014805	XLOC_011583
2	lnc-FAM174B-3	chr15:93014471-93014776	ENSG00000259170.1

No data

Variant related genes	Relation type
C15orf32	TF binding region
C15orf32	CpG island

Extended variants
information (count: 10 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11634493	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12708594	0.83[MEX][hapmap]
rs1869774	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7163161	0.83[MEX][hapmap]
rs7168443	0.87[CEU][hapmap];0.88[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948621	chr15:92688981-93158095	Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1049561	chr15:92758434-93097965	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv1037972	chr15:92804908-93270761	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
4	nsv904499	chr15:92914795-93472582	Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	163 gene(s)	inside rSNPs	diseases
5	nsv519402	chr15:93013560-93015427	Enhancers Weak transcription	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs897466	ZNF774	cis	parietal	SCAN
rs897466	FANCI	cis	parietal	SCAN
rs897466	RHCG	cis	parietal	SCAN
rs897466	SV2B	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93001400-93015800	Weak transcription	Fetal Brain Male	brain
2	chr15:93010200-93015000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr15:93011200-93016600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr15:93011200-93017200	Weak transcription	Fetal Stomach	stomach
5	chr15:93011600-93018000	Weak transcription	HSMMtube	muscle
6	chr15:93011800-93015000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:93011800-93015600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr15:93012800-93015800	Weak transcription	Spleen	Spleen
9	chr15:93012800-93020800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr15:93013000-93016400	Weak transcription	Brain Germinal Matrix	brain
11	chr15:93013200-93017200	Weak transcription	Fetal Brain Female	brain
12	chr15:93013800-93014600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr15:93014400-93015000	Enhancers	HUES6 Cell Line	embryonic stem cell

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