Variant report

Variant	rs4415979
Chromosome Location	chr15:39894495-39894496
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:110)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:110 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr15:39894480-39894630	HRPEpiC	eye:	n/a	n/a
2	CTCF	chr15:39894399-39894671	MCF-7	breast:	n/a	n/a
3	CTCF	chr15:39894442-39894625	A549	lung:	n/a	n/a
4	CTCF	chr15:39894420-39894570	GM12868	blood:	n/a	n/a
5	CTCF	chr15:39894437-39894653	NHEK	skin:	n/a	n/a
6	CTCF	chr15:39894420-39894570	GM12872	blood:	n/a	n/a
7	CTCF	chr15:39894480-39894630	HA-sp	spinal cord:	n/a	n/a
8	CTCF	chr15:39894420-39894570	RPTEC	kidney:	n/a	n/a
9	CTCF	chr15:39894404-39894648	MCF-7	breast:	n/a	n/a
10	CTCF	chr15:39894440-39894684	A549	lung:	n/a	n/a
11	CTCF	chr15:39894480-39894630	Caco-2	colon:	n/a	n/a
12	CTCF	chr15:39894461-39894532	GM13977	blood:	n/a	n/a
13	CTCF	chr15:39894460-39894610	HCT-116	colon:	n/a	n/a
14	CTCF	chr15:39894440-39894590	WERI-Rb-1	eye:	n/a	n/a
15	CTCF	chr15:39894411-39894660	MCF-7	breast:	n/a	n/a
16	ZNF143	chr15:39894374-39894718	H1-hESC	embryonic stem cell:	n/a	n/a
17	CTCF	chr15:39894456-39894626	GM19238	blood:	n/a	n/a
18	RAD21	chr15:39894422-39894635	GM12878	blood:	n/a	n/a
19	CTCF	chr15:39894400-39894550	HCT-116	colon:	n/a	n/a
20	CTCF	chr15:39894480-39894630	AoAF	blood vessel:	n/a	n/a
21	CTCFL	chr15:39894454-39894627	K562	blood:	n/a	n/a
22	CTCF	chr15:39894471-39894620	Hela-S3	cervix:	n/a	n/a
23	CTCF	chr15:39894460-39894610	HFF-Myc	foreskin:	n/a	n/a
24	CTCF	chr15:39894440-39894590	AG04449	skin:	n/a	n/a
25	CTCF	chr15:39894447-39894660	HepG2	liver:	n/a	n/a
26	CTCF	chr15:39894400-39894550	GM12869	blood:	n/a	n/a
27	CTCF	chr15:39894420-39894570	GM12873	blood:	n/a	n/a
28	RAD21	chr15:39894477-39894586	K562	blood:	n/a	n/a
29	CTCF	chr15:39894400-39894550	AG09309	skin:	n/a	n/a
30	CTCF	chr15:39894393-39894615	A549	lung:	n/a	n/a
31	RAD21	chr15:39894374-39894828	MCF-7	breast:	n/a	n/a
32	RAD21	chr15:39894396-39894667	ECC-1	luminal epithelium:	n/a	n/a
33	CTCF	chr15:39894420-39894570	HMEC	breast:	n/a	n/a
34	CTCF	chr15:39894480-39894630	GM12873	blood:	n/a	n/a
35	CTCF	chr15:39894413-39894684	GM12878	blood:	n/a	n/a
36	CTCF	chr15:39894480-39894630	AG04450	lung:	n/a	n/a
37	CTCF	chr15:39894473-39894624	GM19240	blood:	n/a	n/a
38	RAD21	chr15:39894420-39894817	MCF-7	breast:	n/a	n/a
39	TEAD4	chr15:39894319-39894678	H1-hESC	embryonic stem cell:	n/a	n/a
40	CTCF	chr15:39894420-39894570	GM12865	blood:	n/a	n/a
41	CTCF	chr15:39894420-39894570	GM12874	blood:	n/a	n/a
42	CTCF	chr15:39894460-39894610	Caco-2	colon:	n/a	n/a
43	CTCF	chr15:39894440-39894650	K562	blood:	n/a	n/a
44	CTCF	chr15:39894386-39894772	HepG2	liver:	n/a	n/a
45	RAD21	chr15:39894419-39894611	K562	blood:	n/a	n/a
46	CTCF	chr15:39894397-39894737	K562	blood:	n/a	n/a
47	CTCF	chr15:39894440-39894590	HEK293	kidney:	n/a	n/a
48	CTCF	chr15:39894421-39894650	MCF-7	breast:	n/a	n/a
49	CTCF	chr15:39894480-39894630	HRE	kidney:	n/a	n/a
50	CTCF	chr15:39894420-39894570	GM12871	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr15:39885481..39888433-chr15:39892783..39894545,2	K562	blood:
2	chr15:39886322..39888433-chr15:39891587..39894545,2	K562	blood:
3	chr15:39894197..39894999-chr15:40048783..40049685,3	MCF-7	breast:

No data

Variant related genes	Relation type
FSIP1	TF binding region
ENSG00000137801	Chromatin interaction
ENSG00000259279	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10083552	1.00[JPT][hapmap]
rs10152903	1.00[CHB][hapmap]
rs10152951	1.00[CHB][hapmap]
rs1038097	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1051442	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10520141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10520143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10520145	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10520146	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10520147	1.00[CHB][hapmap]
rs10520148	1.00[CHB][hapmap];0.91[MEX][hapmap]
rs10520152	1.00[JPT][hapmap]
rs1073675	1.00[CHB][hapmap]
rs12324682	1.00[JPT][hapmap]
rs1382443	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1382444	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16969167	1.00[CHB][hapmap]
rs16969335	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16969338	1.00[JPT][hapmap]
rs16969352	1.00[JPT][hapmap]
rs16969487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16969491	0.86[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16969547	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16969663	1.00[CHB][hapmap]
rs16969664	1.00[CHB][hapmap]
rs16969666	1.00[CHB][hapmap]
rs16969672	1.00[CHB][hapmap]
rs16969679	1.00[CHB][hapmap]
rs16969680	1.00[CHB][hapmap]
rs16969688	1.00[CHB][hapmap]
rs17632916	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17633107	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17633210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17705806	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17706083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17706179	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1813493	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1988082	0.82[EUR][1000 genomes]
rs1988555	0.85[EUR][1000 genomes]
rs1994380	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2129457	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2228262	1.00[CHB][hapmap]
rs2228263	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2411316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2618156	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2618160	0.92[EUR][1000 genomes]
rs2618161	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2618164	1.00[CEU][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes]
rs2618165	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs2618167	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2664123	0.92[EUR][1000 genomes]
rs2664136	0.92[EUR][1000 genomes]
rs2664137	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2664138	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs2664140	0.92[EUR][1000 genomes]
rs2664142	0.92[EUR][1000 genomes]
rs28377784	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28549326	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28619289	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28653011	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34878675	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs41315060	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4319740	0.83[CEU][hapmap]
rs4503768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs45461294	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4923835	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs58188999	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59578395	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59628570	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6492905	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7172155	1.00[CHB][hapmap]
rs7173948	1.00[CHB][hapmap]
rs7179604	1.00[CHB][hapmap]
rs7181354	1.00[CHB][hapmap]
rs7182423	1.00[CHB][hapmap]
rs74008647	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs74008648	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8036035	1.00[JPT][hapmap]
rs8041266	1.00[CHB][hapmap]
rs880270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs937961	1.00[CHB][hapmap]
rs937962	1.00[CHB][hapmap]
rs954152	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9972350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv904094	chr15:39738006-39976057	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv832977	chr15:39817512-39981520	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1048628	chr15:39877498-39940104	Enhancers Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1502	chr15:39884314-39928968	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39888400-39899200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:39888400-39899200	Weak transcription	Esophagus	oesophagus
3	chr15:39888400-39899200	Weak transcription	Left Ventricle	heart
4	chr15:39888400-39900600	Weak transcription	Fetal Brain Female	brain
5	chr15:39888400-39901000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:39888400-39901000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr15:39889200-39901200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr15:39890200-39900800	Weak transcription	HMEC	breast
9	chr15:39890600-39897000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr15:39892200-39899200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr15:39892600-39897800	Weak transcription	Osteobl	bone
12	chr15:39892800-39896800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr15:39892800-39896800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr15:39894400-39894600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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