Variant report

Variant	rs12565272
Chromosome Location	chr1:75598070-75598071
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:122)
Chromatin interactive
region (count:0)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SUZ12	chr1:75595125-75598694	H1-hESC	embryonic stem cell:	n/a	n/a
2	SUZ12	chr1:75594519-75601637	NT2-D1	testis:	n/a	n/a
3	POLR2A	chr1:75596570-75599860	H1-neurons	neurons:	n/a	n/a
4	TCF12	chr1:75597948-75598166	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr1:75596503-75602546	H1-neurons	neurons:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:75598039-75598089	HEK293	kidney:	embryo
2	chr1:75598039-75598089	HEEpiC	esophagus:	n/a
3	chr1:75598070-75598120	Hela-S3	cervix:	n/a
4	chr1:75598070-75598120	HCF	heart:	n/a
5	chr1:75598039-75598089	NHBE	bronchial:	n/a
6	chr1:75598070-75598120	HEEpiC	esophagus:	n/a
7	chr1:75598039-75598089	GM12892	blood:	n/a
8	chr1:75598070-75598120	HCT-116	colon:	n/a
9	chr1:75598070-75598120	PFSK-1	brain:	n/a
10	chr1:75598070-75598120	NHBE	bronchial:	n/a
11	chr1:75598070-75598120	AG04450	lung:	fetal
12	chr1:75598070-75598120	PANC-1	pancreas:	n/a
13	chr1:75598039-75598089	ProgFib	skin:	n/a
14	chr1:75598070-75598120	HRCEpiC	kidney:	n/a
15	chr1:75598070-75598120	AG10803	skin:	n/a
16	chr1:75598039-75598089	GM12878	blood:	n/a
17	chr1:75598039-75598089	SK-N-MC	brain:	n/a
18	chr1:75598070-75598120	CMK	blood:	n/a
19	chr1:75598039-75598089	GM12891	blood:	n/a
20	chr1:75598070-75598120	K562	blood:	n/a
21	chr1:75598039-75598089	HMEC	breast:	n/a
22	chr1:75598070-75598120	HRE	kidney:	n/a
23	chr1:75598039-75598089	NB4	blood:	n/a
24	chr1:75598070-75598120	SK-N-MC	brain:	n/a
25	chr1:75598039-75598089	MCF10A-Er-Src	breast:	n/a
26	chr1:75598070-75598120	HepG2	liver:	n/a
27	chr1:75598039-75598089	HRE	kidney:	n/a
28	chr1:75598039-75598089	SAEC	small airway:	n/a
29	chr1:75598070-75598120	SK-N-SH_RA	brain:	n/a
30	chr1:75598039-75598089	T-47D	breast:	n/a
31	chr1:75598070-75598120	SKMC	muscle:	n/a
32	chr1:75598039-75598089	AoSMC	blood vessel:	n/a
33	chr1:75598039-75598089	Hepatocyte	liver:	n/a
34	chr1:75598070-75598120	Jurkat	blood:	n/a
35	chr1:75598070-75598120	Hepatocyte	liver:	n/a
36	chr1:75598039-75598089	BE2_C	brain:	n/a
37	chr1:75598039-75598089	AG04450	lung:	fetal
38	chr1:75598039-75598089	PANC-1	pancreas:	n/a
39	chr1:75598070-75598120	BJ	skin:	n/a
40	chr1:75598070-75598120	MCF10A-Er-Src	breast:	n/a
41	chr1:75598039-75598089	HUVEC	blood vessel:	n/a
42	chr1:75598039-75598089	PFSK-1	brain:	n/a
43	chr1:75598070-75598120	SK-N-SH	brain:	n/a
44	chr1:75598070-75598120	HUVEC	blood vessel:	n/a
45	chr1:75598070-75598120	T-47D	breast:	n/a
46	chr1:75598039-75598089	HepG2	liver:	n/a
47	chr1:75598039-75598089	MCF-7	breast:	n/a
48	chr1:75598039-75598089	A549	lung:	n/a
49	chr1:75598039-75598089	SK-N-SH	brain:	n/a
50	chr1:75598070-75598120	SAEC	small airway:	n/a

No data

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC44A5-1	chr1:75598039-75598261	ENSG00000224149.1

No data

Variant related genes	Relation type
LHX8	TF binding region
LHX8	CpG island

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1007512	0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs10493552	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10493553	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11162513	0.91[ASN][1000 genomes]
rs11162567	0.87[ASN][1000 genomes]
rs12036667	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12041465	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12563445	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1526504	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1526505	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1526507	0.91[ASN][1000 genomes]
rs1526513	0.89[ASN][1000 genomes]
rs17096272	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs17096289	0.87[ASN][1000 genomes]
rs1852347	0.89[ASN][1000 genomes]
rs4949725	0.89[ASN][1000 genomes]
rs7520936	0.91[ASN][1000 genomes]
rs7535534	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871743	chr1:75235082-75714554	Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv3368999	chr1:75524762-75933220	Bivalent/Poised TSS Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75596000-75600600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
2	chr1:75596200-75598200	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:75596400-75600200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr1:75597400-75598200	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:75597400-75599400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
6	chr1:75597600-75598200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
7	chr1:75597600-75598200	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:75597600-75598200	Bivalent Enhancer	Brain Germinal Matrix	brain
9	chr1:75597800-75598200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
10	chr1:75597800-75598800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:75598000-75598200	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
12	chr1:75598000-75598200	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:75598000-75598200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
14	chr1:75598000-75598200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
15	chr1:75598000-75598200	Bivalent Enhancer	Stomach Smooth Muscle	stomach
16	chr1:75598000-75598400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
17	chr1:75598000-75598600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
18	chr1:75598000-75599000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell

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