Variant report

Variant	rs55788652
Chromosome Location	chr4:165858788-165858789
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:24)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:24 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr4:165858779-165859480	GM12878	blood:	n/a	n/a
2	MAFK	chr4:165858725-165859304	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr4:165858760-165858910	HRPEpiC	eye:	n/a	n/a
4	POLR2A	chr4:165858657-165859078	SK-N-MC	brain:	n/a	n/a
5	CTCF	chr4:165858740-165858890	HCM	heart:	n/a	n/a
6	WRNIP1	chr4:165858753-165860017	GM12878	blood:	n/a	n/a
7	CTCF	chr4:165858740-165858890	NHLF	lung:	n/a	n/a
8	CTCF	chr4:165858760-165858910	GM12875	blood:	n/a	n/a
9	RAD21	chr4:165858715-165859403	H1-hESC	embryonic stem cell:	n/a	n/a
10	RAD21	chr4:165858722-165859504	HCT-116	colon:	n/a	n/a
11	TBP	chr4:165856452-165859552	GM12878	blood:	n/a	n/a
12	RAD21	chr4:165858691-165859458	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr4:165858785-165859047	NHEK	skin:	n/a	n/a
14	CTCF	chr4:165858760-165858910	NHDF-neo	bronchial:	n/a	n/a
15	CTCF	chr4:165858723-165859065	H1-hESC	embryonic stem cell:	n/a	n/a
16	RAD21	chr4:165858633-165859483	H1-hESC	embryonic stem cell:	n/a	n/a
17	CHD1	chr4:165858664-165859460	GM12878	blood:	n/a	n/a
18	CTCF	chr4:165858700-165858850	HVMF	connective:	n/a	n/a
19	CTCF	chr4:165858785-165859026	LNCaP	prostate:	n/a	n/a
20	MAFK	chr4:165858776-165858976	HepG2	liver:	n/a	n/a
21	POLR2A	chr4:165858779-165859417	GM12878	blood:	n/a	n/a
22	MAFK	chr4:165858721-165858984	K562	blood:	n/a	n/a
23	CTCF	chr4:165858721-165859477	GM12878	blood:	n/a	n/a
24	CTCF	chr4:165858772-165859390	H1-hESC	embryonic stem cell:	n/a	n/a

No data

Variant related genes	Relation type
ENSG00000270960	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10001924	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10002601	0.83[ASN][1000 genomes]
rs10016502	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10020142	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10020204	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10025595	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11939364	0.87[ASN][1000 genomes]
rs11941364	0.86[ASN][1000 genomes]
rs12501482	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28544252	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4359860	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4380479	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4396952	0.86[ASN][1000 genomes]
rs55724447	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56725431	0.81[AMR][1000 genomes]
rs59310432	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6848177	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72697944	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7663962	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7664173	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461821	chr4:165402309-165859951	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv596037	chr4:165402309-165859951	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1019150	chr4:165505585-165907924	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv1026152	chr4:165622244-166027447	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv537336	chr4:165622244-166027447	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	nsv1022210	chr4:165792630-166251612	Genic enhancers Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	nsv537337	chr4:165792630-166251612	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	nsv880382	chr4:165793001-165964290	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
9	esv2757965	chr4:165801816-165976350	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
10	esv2759299	chr4:165801816-165976350	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers 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	27 gene(s)	inside rSNPs	diseases
11	nsv528686	chr4:165814359-165930168	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
12	nsv967697	chr4:165843736-165889668	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv1015970	chr4:165852926-165973078	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
14	nsv1021905	chr4:165852926-166212878	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
15	nsv830140	chr4:165855999-165956612	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
16	nsv822815	chr4:165858272-165862356	Enhancers Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:165855200-165858800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr4:165857400-165859400	Flanking Active TSS	GM12878-XiMat	blood
3	chr4:165857600-165859200	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr4:165857600-165859200	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr4:165857600-165859200	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr4:165857600-165859200	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr4:165857800-165859200	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr4:165857800-165859200	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr4:165858000-165859200	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr4:165858600-165859000	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr4:165858600-165859000	Enhancers	Adipose Nuclei	Adipose
12	chr4:165858600-165859200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
13	chr4:165858600-165859200	Enhancers	HSMMtube	muscle
14	chr4:165858600-165859400	Enhancers	Fetal Muscle Leg	muscle

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