Variant report

Variant	rs12442758
Chromosome Location	chr15:34506111-34506112
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:22 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr15:34506040-34506190	HCM	heart:	n/a	chr15:34506048-34506069
2	SIN3A	chr15:34506032-34506866	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr15:34505980-34506130	HBMEC	blood vessel:	n/a	chr15:34506048-34506069
4	CTCF	chr15:34506000-34506150	HRPEpiC	eye:	n/a	chr15:34506048-34506069
5	CTCF	chr15:34506033-34506135	GM19240	blood:	n/a	chr15:34506048-34506069
6	CTCF	chr15:34505980-34506130	HepG2	liver:	n/a	chr15:34506048-34506069
7	CTCF	chr15:34506040-34506111	GM12892	blood:	n/a	chr15:34506048-34506069
8	CTCF	chr15:34505956-34506156	K562	blood:	n/a	chr15:34506048-34506069
9	CTCF	chr15:34506027-34506117	MCF-7	breast:	n/a	chr15:34506048-34506069
10	CTCF	chr15:34505980-34506130	GM12873	blood:	n/a	chr15:34506048-34506069
11	CTCF	chr15:34506020-34506170	HMF	breast:	n/a	chr15:34506048-34506069
12	CTCF	chr15:34505980-34506130	HCPEpiC	choroid plexus:	n/a	chr15:34506048-34506069
13	CTCF	chr15:34506000-34506150	HCFaa	heart:	n/a	chr15:34506048-34506069
14	CTCF	chr15:34506003-34506140	Hela-S3	cervix:	n/a	chr15:34506048-34506069
15	CTCF	chr15:34505980-34506130	Hela-S3	cervix:	n/a	chr15:34506048-34506069
16	ZNF143	chr15:34506039-34506841	H1-hESC	embryonic stem cell:	n/a	n/a
17	CTCF	chr15:34506005-34506118	MCF-7	breast:	n/a	chr15:34506048-34506069
18	CTCF	chr15:34505980-34506130	WERI-Rb-1	eye:	n/a	chr15:34506048-34506069
19	CTCF	chr15:34506020-34506170	GM12864	blood:	n/a	chr15:34506048-34506069
20	CTCF	chr15:34505918-34506187	GM12878	blood:	n/a	chr15:34506048-34506069
21	CTCF	chr15:34506020-34506170	HRE	kidney:	n/a	chr15:34506048-34506069
22	MAX	chr15:34506032-34506749	H1-hESC	embryonic stem cell:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:34506071-34506121	H1-hESC	embryonic stem cell:	embryo
2	chr15:34506071-34506121	GM12891	blood:	n/a
3	chr15:34506071-34506121	AG04449	skin:	fetal
4	chr15:34506071-34506121	NH-A	brain:	n/a
5	chr15:34506071-34506121	PrEC	prostate:	n/a
6	chr15:34506071-34506121	SK-N-SH_RA	brain:	n/a
7	chr15:34506071-34506121	HPAEpiC	pulmonary alveolar:	n/a
8	chr15:34506071-34506121	HCM	heart:	n/a
9	chr15:34506071-34506121	HAEpiC	amniotic membrane:	n/a
10	chr15:34506071-34506121	LNCaP	prostate:	n/a
11	chr15:34506071-34506121	CMK	blood:	n/a
12	chr15:34506071-34506121	MCF-7	breast:	n/a
13	chr15:34506071-34506121	AG09309	skin:	n/a
14	chr15:34506071-34506121	Hepatocyte	liver:	n/a
15	chr15:34506071-34506121	ProgFib	skin:	n/a
16	chr15:34506071-34506121	PANC-1	pancreas:	n/a
17	chr15:34506071-34506121	Jurkat	blood:	n/a
18	chr15:34506071-34506121	HCF	heart:	n/a
19	chr15:34506071-34506121	HIPEpiC	eye:	n/a
20	chr15:34506071-34506121	U87	brain:	n/a
21	chr15:34506071-34506121	HEEpiC	esophagus:	n/a
22	chr15:34506071-34506121	SAEC	small airway:	n/a
23	chr15:34506071-34506121	GM12878	blood:	n/a
24	chr15:34506071-34506121	NHBE	bronchial:	n/a
25	chr15:34506071-34506121	A549	lung:	n/a
26	chr15:34506071-34506121	NB4	blood:	n/a
27	chr15:34506071-34506121	GM06990	blood:	n/a
28	chr15:34506071-34506121	AG04450	lung:	fetal
29	chr15:34506071-34506121	HRCEpiC	kidney:	n/a
30	chr15:34506071-34506121	NT2-D1	testis:	n/a
31	chr15:34506071-34506121	HL-60	blood:	n/a
32	chr15:34506071-34506121	GM19239	blood:	n/a
33	chr15:34506071-34506121	SK-N-MC	brain:	n/a
34	chr15:34506071-34506121	GM12892	blood:	n/a
35	chr15:34506071-34506121	HNPCEpiC	eye:	n/a
36	chr15:34506071-34506121	AG10803	skin:	n/a
37	chr15:34506071-34506121	Hela-S3	cervix:	n/a
38	chr15:34506071-34506121	T-47D	breast:	n/a
39	chr15:34506071-34506121	IMR90	lung:	fetal
40	chr15:34506071-34506121	BJ	skin:	n/a
41	chr15:34506071-34506121	K562	blood:	n/a
42	chr15:34506071-34506121	ECC-1	luminal epithelium:	n/a
43	chr15:34506071-34506121	BE2_C	brain:	n/a
44	chr15:34506071-34506121	HMEC	breast:	n/a
45	chr15:34506071-34506121	RPTEC	kidney:	n/a
46	chr15:34506071-34506121	ovcar-3	ovarian:	n/a
47	chr15:34506071-34506121	HCT-116	colon:	n/a
48	chr15:34506071-34506121	SKMC	muscle:	n/a
49	chr15:34506071-34506121	HRE	kidney:	n/a
50	chr15:34506071-34506121	PFSK-1	brain:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr15:34500965..34503586-chr15:34505222..34506873,2	K562	blood:
2	chr15:34402294..34404744-chr15:34506028..34509076,3	MCF-7	breast:
3	chr15:34505937..34506527-chr15:34659469..34660347,2	MCF-7	breast:
4	chr15:34504430..34506466-chr15:34515218..34517671,3	K562	blood:

No data

Variant related genes	Relation type
KATNBL1	TF binding region
KATNBL1	CpG island
ENSG00000134152	Chromatin interaction
ENSG00000128463	Chromatin interaction
ENSG00000176454	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10851952	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10851955	0.94[ASN][1000 genomes]
rs11073010	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11073014	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11073019	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11631981	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11635964	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11854686	0.85[ASN][1000 genomes]
rs11857205	0.85[ASN][1000 genomes]
rs11858408	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12437551	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12441003	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12591315	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12917397	0.95[ASN][1000 genomes]
rs1978810	0.85[ASN][1000 genomes]
rs28652966	0.90[ASN][1000 genomes]
rs4381574	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4780227	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4780229	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4780232	0.83[EUR][1000 genomes]
rs56731918	0.89[ASN][1000 genomes]
rs57502425	0.83[ASN][1000 genomes]
rs58875083	0.89[ASN][1000 genomes]
rs6495619	0.84[ASN][1000 genomes]
rs6495620	0.82[ASN][1000 genomes]
rs6495621	0.85[ASN][1000 genomes]
rs6495625	0.87[ASN][1000 genomes]
rs7164448	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7168619	0.83[ASN][1000 genomes]
rs7168761	0.83[ASN][1000 genomes]
rs7174014	0.84[ASN][1000 genomes]
rs7178988	0.89[ASN][1000 genomes]
rs7180200	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7181687	0.89[ASN][1000 genomes]
rs7181902	0.89[ASN][1000 genomes]
rs8026939	0.90[ASN][1000 genomes]
rs8027499	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8027830	0.89[ASN][1000 genomes]
rs8028027	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8034315	0.89[ASN][1000 genomes]
rs8036468	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8040071	0.87[ASN][1000 genomes]
rs8041586	0.80[ASN][1000 genomes]
rs8041977	0.86[ASN][1000 genomes]
rs8043216	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9972505	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052804	chr15:34498529-34841447	Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv542341	chr15:34498529-34841447	Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1045173	chr15:34501055-34596995	Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:34502600-34506200	Weak transcription	Fetal Thymus	thymus
2	chr15:34502600-34510000	Weak transcription	NHLF	lung
3	chr15:34503600-34506600	Weak transcription	K562	blood
4	chr15:34504400-34506200	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr15:34504600-34506400	Enhancers	H1 Cell Line	embryonic stem cell
6	chr15:34504600-34507200	Enhancers	H9 Cell Line	embryonic stem cell
7	chr15:34504800-34506400	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr15:34505000-34510200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr15:34505200-34506200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr15:34505800-34506200	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr15:34506000-34506200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr15:34506000-34506200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr15:34506000-34507000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr15:34506000-34507000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr15:34506000-34507200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr15:34506000-34507200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links