Variant report

Variant	rs62571046
Chromosome Location	chr9:15527864-15527865
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:15527211-15527975	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr9:15527384-15527896	Hela-S3	cervix:	n/a	n/a
3	HEY1	chr9:15527512-15527915	HepG2	liver:	n/a	chr9:15527720-15527735 chr9:15527709-15527724 chr9:15527697-15527712
4	POLR2A	chr9:15527330-15528041	GM12892	blood:	n/a	n/a
5	POLR2A	chr9:15527326-15528011	GM12878	blood:	n/a	n/a
6	HEY1	chr9:15527474-15527897	K562	blood:	n/a	chr9:15527720-15527735 chr9:15527709-15527724 chr9:15527697-15527712
7	POLR2A	chr9:15527485-15527865	GM12878	blood:	n/a	n/a
8	POLR2A	chr9:15527765-15527881	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr9:15527360-15527919	Hela-S3	cervix:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr9:15527817-15527867	MCF10A-Er-Src	breast:	n/a
2	chr9:15527817-15527867	NH-A	brain:	n/a
3	chr9:15527817-15527867	PrEC	prostate:	n/a
4	chr9:15527817-15527867	SAEC	small airway:	n/a
5	chr9:15527817-15527867	CMK	blood:	n/a
6	chr9:15527817-15527867	H1-hESC	embryonic stem cell:	embryo
7	chr9:15527817-15527867	HUVEC	blood vessel:	n/a
8	chr9:15527817-15527867	U87	brain:	n/a
9	chr9:15527817-15527867	GM12878	blood:	n/a
10	chr9:15527817-15527867	NHDF-neo	bronchial:	n/a
11	chr9:15527817-15527867	SKMC	muscle:	n/a
12	chr9:15527817-15527867	BJ	skin:	n/a
13	chr9:15527817-15527867	RPTEC	kidney:	n/a
14	chr9:15527817-15527867	NT2-D1	testis:	n/a
15	chr9:15527817-15527867	AG09309	skin:	n/a
16	chr9:15527817-15527867	HL-60	blood:	n/a
17	chr9:15527817-15527867	NHBE	bronchial:	n/a
18	chr9:15527817-15527867	GM12892	blood:	n/a
19	chr9:15527817-15527867	ECC-1	luminal epithelium:	n/a
20	chr9:15527817-15527867	NB4	blood:	n/a
21	chr9:15527817-15527867	GM19239	blood:	n/a
22	chr9:15527817-15527867	HepG2	liver:	n/a
23	chr9:15527817-15527867	LNCaP	prostate:	n/a
24	chr9:15527817-15527867	Jurkat	blood:	n/a
25	chr9:15527817-15527867	HCF	heart:	n/a
26	chr9:15527817-15527867	AG04449	skin:	fetal
27	chr9:15527817-15527867	ProgFib	skin:	n/a
28	chr9:15527817-15527867	A549	lung:	n/a
29	chr9:15527817-15527867	IMR90	lung:	fetal
30	chr9:15527817-15527867	HMEC	breast:	n/a
31	chr9:15527817-15527867	K562	blood:	n/a
32	chr9:15527817-15527867	HNPCEpiC	eye:	n/a
33	chr9:15527817-15527867	AG04450	lung:	fetal
34	chr9:15527817-15527867	HIPEpiC	eye:	n/a
35	chr9:15527817-15527867	BE2_C	brain:	n/a
36	chr9:15527817-15527867	Caco-2	colon:	n/a
37	chr9:15527817-15527867	MCF-7	breast:	n/a
38	chr9:15527817-15527867	Hela-S3	cervix:	n/a
39	chr9:15527817-15527867	SK-N-MC	brain:	n/a
40	chr9:15527817-15527867	AG10803	skin:	n/a
41	chr9:15527817-15527867	HCPEpiC	choroid plexus:	n/a
42	chr9:15527817-15527867	T-47D	breast:	n/a
43	chr9:15527817-15527867	PANC-1	pancreas:	n/a
44	chr9:15527817-15527867	Hepatocyte	liver:	n/a
45	chr9:15527817-15527867	ovcar-3	ovarian:	n/a
46	chr9:15527817-15527867	AG09319	gingival:	n/a
47	chr9:15527817-15527867	SK-N-SH_RA	brain:	n/a
48	chr9:15527817-15527867	HCT-116	colon:	n/a
49	chr9:15527817-15527867	HEK293	kidney:	embryo
50	chr9:15527817-15527867	HRE	kidney:	n/a

No data

Variant related genes	Relation type
RN7SL98P	TF binding region
FTH1P12	TF binding region
FTH1P12	CpG island
RN7SL98P	CpG island

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10810392	0.84[AFR][1000 genomes]
rs10810393	0.83[AFR][1000 genomes]
rs10810394	0.84[AFR][1000 genomes]
rs16933296	0.81[EUR][1000 genomes]
rs16933350	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3087653	0.85[EUR][1000 genomes]
rs41268961	0.85[EUR][1000 genomes]
rs41306098	0.85[EUR][1000 genomes]
rs58168894	0.90[AFR][1000 genomes]
rs59355275	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59520337	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62570969	0.81[EUR][1000 genomes]
rs62570972	0.81[EUR][1000 genomes]
rs62570976	0.80[EUR][1000 genomes]
rs62570980	0.85[EUR][1000 genomes]
rs62570991	0.85[EUR][1000 genomes]
rs62570992	0.85[EUR][1000 genomes]
rs62570993	0.85[EUR][1000 genomes]
rs62571001	0.81[EUR][1000 genomes]
rs62571002	0.81[EUR][1000 genomes]
rs62571003	0.83[EUR][1000 genomes]
rs62571007	0.85[EUR][1000 genomes]
rs62571008	0.83[EUR][1000 genomes]
rs62571009	0.85[EUR][1000 genomes]
rs62571011	0.85[EUR][1000 genomes]
rs62571015	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62571016	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62571017	0.95[EUR][1000 genomes]
rs62571018	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62571029	0.90[EUR][1000 genomes]
rs62571033	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62571037	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62571047	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62571048	1.00[EUR][1000 genomes]
rs62571050	0.92[EUR][1000 genomes]
rs62571051	0.90[EUR][1000 genomes]
rs62571052	0.87[EUR][1000 genomes]
rs73410204	0.95[AFR][1000 genomes]
rs73410215	0.90[AFR][1000 genomes]
rs7856523	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7856657	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]

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	nsv517975	chr9:15286446-15534070	Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv892625	chr9:15326251-16064850	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv892626	chr9:15389610-15694690	Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv892627	chr9:15397969-15909450	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv892628	chr9:15420805-15528290	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv892629	chr9:15516375-15634326	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62571046	PSIP1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15523000-15528200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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