Variant report

Variant	rs62310884
Chromosome Location	chr4:56458400-56458401
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CCNT2	chr4:56458211-56458608	K562	blood:	n/a	n/a
2	CHD2	chr4:56458300-56458479	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr4:56458316-56458518	H1-hESC	embryonic stem cell:	n/a	n/a
4	HMGN3	chr4:56458288-56458550	K562	blood:	n/a	n/a
5	POLR2A	chr4:56457051-56461679	K562	blood:	n/a	n/a
6	POLR2A	chr4:56457732-56460674	K562	blood:	n/a	n/a
7	POLR2A	chr4:56458188-56459394	K562	blood:	n/a	n/a
8	CTCF	chr4:56458266-56458488	H1-hESC	embryonic stem cell:	n/a	n/a
9	RAD21	chr4:56458146-56458628	H1-hESC	embryonic stem cell:	n/a	chr4:56458309-56458323 chr4:56458514-56458528 chr4:56458369-56458383
10	RCOR1	chr4:56458381-56458458	K562	blood:	n/a	n/a
11	RAD21	chr4:56458197-56458555	H1-hESC	embryonic stem cell:	n/a	chr4:56458309-56458323 chr4:56458514-56458528 chr4:56458369-56458383
12	POLR2A	chr4:56458002-56460867	K562	blood:	n/a	n/a
13	RAD21	chr4:56458234-56458549	H1-hESC	embryonic stem cell:	n/a	chr4:56458309-56458323 chr4:56458514-56458528 chr4:56458369-56458383
14	POLR2A	chr4:56458102-56459026	K562	blood:	n/a	n/a
15	POLR2A	chr4:56458063-56459419	K562	blood:	n/a	n/a
16	POLR2A	chr4:56458265-56459048	K562	blood:	n/a	n/a
17	POLR2A	chr4:56458085-56461042	K562	blood:	n/a	n/a
18	POLR2A	chr4:56458216-56461090	K562	blood:	n/a	n/a
19	CTCF	chr4:56458280-56458500	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	chr4:56458370-56458420	SK-N-SH_RA	brain:	n/a
2	chr4:56458370-56458420	AG04450	lung:	fetal
3	chr4:56458370-56458420	Caco-2	colon:	n/a
4	chr4:56458370-56458420	SK-N-SH	brain:	n/a
5	chr4:56458370-56458420	NHBE	bronchial:	n/a
6	chr4:56458370-56458420	GM12878	blood:	n/a
7	chr4:56458370-56458420	HIPEpiC	eye:	n/a
8	chr4:56458370-56458420	MCF10A-Er-Src	breast:	n/a
9	chr4:56458370-56458420	HAEpiC	amniotic membrane:	n/a
10	chr4:56458370-56458420	HCT-116	colon:	n/a
11	chr4:56458370-56458420	AG09309	skin:	n/a
12	chr4:56458370-56458420	HCPEpiC	choroid plexus:	n/a
13	chr4:56458370-56458420	ovcar-3	ovarian:	n/a
14	chr4:56458370-56458420	PANC-1	pancreas:	n/a
15	chr4:56458370-56458420	AoSMC	blood vessel:	n/a
16	chr4:56458370-56458420	ProgFib	skin:	n/a
17	chr4:56458370-56458420	GM12892	blood:	n/a
18	chr4:56458370-56458420	HL-60	blood:	n/a
19	chr4:56458370-56458420	HCM	heart:	n/a
20	chr4:56458370-56458420	H1-hESC	embryonic stem cell:	embryo
21	chr4:56458370-56458420	HepG2	liver:	n/a
22	chr4:56458370-56458420	NHDF-neo	bronchial:	n/a
23	chr4:56458370-56458420	AG09319	gingival:	n/a
24	chr4:56458370-56458420	HPAEpiC	pulmonary alveolar:	n/a
25	chr4:56458370-56458420	NB4	blood:	n/a
26	chr4:56458370-56458420	Jurkat	blood:	n/a
27	chr4:56458370-56458420	HRPEpiC	eye:	n/a
28	chr4:56458370-56458420	SK-N-MC	brain:	n/a
29	chr4:56458370-56458420	IMR90	lung:	fetal
30	chr4:56458370-56458420	RPTEC	kidney:	n/a
31	chr4:56458370-56458420	AG04449	skin:	fetal
32	chr4:56458370-56458420	GM12891	blood:	n/a
33	chr4:56458370-56458420	PFSK-1	brain:	n/a
34	chr4:56458370-56458420	CMK	blood:	n/a
35	chr4:56458370-56458420	HRCEpiC	kidney:	n/a
36	chr4:56458370-56458420	GM06990	blood:	n/a
37	chr4:56458370-56458420	Hepatocyte	liver:	n/a
38	chr4:56458370-56458420	HEEpiC	esophagus:	n/a
39	chr4:56458370-56458420	HMEC	breast:	n/a
40	chr4:56458370-56458420	SAEC	small airway:	n/a
41	chr4:56458370-56458420	GM19239	blood:	n/a
42	chr4:56458370-56458420	HEK293	kidney:	embryo
43	chr4:56458370-56458420	NT2-D1	testis:	n/a
44	chr4:56458370-56458420	HUVEC	blood vessel:	n/a
45	chr4:56458370-56458420	HNPCEpiC	eye:	n/a
46	chr4:56458370-56458420	BJ	skin:	n/a
47	chr4:56458370-56458420	T-47D	breast:	n/a
48	chr4:56458370-56458420	HRE	kidney:	n/a
49	chr4:56458370-56458420	K562	blood:	n/a
50	chr4:56458370-56458420	A549	lung:	n/a

No data

Variant related genes	Relation type
PDCL2	TF binding region
PDCL2	CpG island

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10000512	0.86[ASN][1000 genomes]
rs10011801	0.86[ASN][1000 genomes]
rs10017749	0.81[ASN][1000 genomes]
rs10018932	0.86[ASN][1000 genomes]
rs10026315	0.81[ASN][1000 genomes]
rs10026676	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10029142	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13133077	0.81[ASN][1000 genomes]
rs13434995	0.84[ASN][1000 genomes]
rs17725110	0.83[ASN][1000 genomes]
rs17725163	0.81[ASN][1000 genomes]
rs17781708	0.81[ASN][1000 genomes]
rs1873090	0.81[ASN][1000 genomes]
rs1873091	0.83[ASN][1000 genomes]
rs2101476	0.81[ASN][1000 genomes]
rs2130038	0.81[ASN][1000 genomes]
rs2412658	0.81[ASN][1000 genomes]
rs2412659	0.81[ASN][1000 genomes]
rs2412661	0.81[ASN][1000 genomes]
rs2412664	0.81[ASN][1000 genomes]
rs2412665	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2412666	0.83[ASN][1000 genomes]
rs28416150	0.81[ASN][1000 genomes]
rs28435401	0.86[ASN][1000 genomes]
rs28451532	0.86[ASN][1000 genomes]
rs28473211	0.81[ASN][1000 genomes]
rs28564902	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28708716	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28713371	0.84[ASN][1000 genomes]
rs28756087	0.86[ASN][1000 genomes]
rs34299771	0.88[ASN][1000 genomes]
rs3805383	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3805385	0.81[ASN][1000 genomes]
rs3805387	0.81[ASN][1000 genomes]
rs3805388	0.81[ASN][1000 genomes]
rs3805389	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4336288	0.81[ASN][1000 genomes]
rs55849318	0.81[ASN][1000 genomes]
rs56152424	0.81[ASN][1000 genomes]
rs56288855	0.86[ASN][1000 genomes]
rs57178140	0.81[ASN][1000 genomes]
rs62308665	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62308667	0.81[ASN][1000 genomes]
rs62310862	0.81[ASN][1000 genomes]
rs62310866	0.81[ASN][1000 genomes]
rs6830728	0.81[ASN][1000 genomes]
rs6848755	0.81[ASN][1000 genomes]
rs716806	0.81[ASN][1000 genomes]
rs73236153	0.81[ASN][1000 genomes]
rs73236165	0.81[ASN][1000 genomes]
rs7665286	0.81[ASN][1000 genomes]
rs7665846	0.81[ASN][1000 genomes]
rs7683997	0.81[ASN][1000 genomes]
rs9790448	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9993599	0.81[ASN][1000 genomes]
rs9996936	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[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	esv3328582	chr4:56164136-56486156	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	esv2755990	chr4:56317136-57143037	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv10496	chr4:56336946-56841137	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv998179	chr4:56425126-56694339	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv932636	chr4:56438618-56667329	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56441200-56464400	Weak transcription	K562	blood
2	chr4:56456200-56458400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:56458000-56458400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr4:56458200-56458600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:56458200-56458600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr4:56458400-56458600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:56458400-56458600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived

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