Variant report

Variant	rs5024580
Chromosome Location	chr2:152265280-152265281
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SP1	chr2:152265196-152265776	H1-hESC	embryonic stem cell:	n/a	n/a
2	SP1	chr2:152265190-152265757	H1-hESC	embryonic stem cell:	n/a	n/a
3	RAD21	chr2:152265225-152265547	H1-hESC	embryonic stem cell:	n/a	n/a
4	EP300	chr2:152265203-152265689	H1-hESC	embryonic stem cell:	n/a	n/a
5	CREB1	chr2:152265262-152265660	H1-hESC	embryonic stem cell:	n/a	n/a
6	TEAD4	chr2:152265253-152265759	H1-hESC	embryonic stem cell:	n/a	n/a
7	RAD21	chr2:152265206-152265666	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:152144813..152149803-chr2:152261382..152268379,11	K562	blood:
2	chr2:152262551..152270893-chr2:152273971..152280003,13	K562	blood:
3	chr2:152116678..152120470-chr2:152265032..152268454,8	MCF-7	breast:
4	chr2:152146157..152147960-chr2:152264680..152266212,2	K562	blood:
5	chr2:152116022..152119511-chr2:152263980..152267786,5	K562	blood:
6	chr2:152258517..152261136-chr2:152264603..152266295,2	K562	blood:

No data

Variant related genes	Relation type
RIF1	TF binding region
ENSG00000184898	Chromatin interaction
ENSG00000080345	Chromatin interaction
ENSG00000123609	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10173699	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10175134	0.83[EUR][1000 genomes]
rs10183099	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10206635	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1047957	0.84[EUR][1000 genomes]
rs10490521	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11675385	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12616688	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12616740	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12618981	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12994320	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13555	0.84[EUR][1000 genomes]
rs17193268	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17806204	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2288193	0.83[EUR][1000 genomes]
rs2342911	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2432942	0.81[ASN][1000 genomes]
rs2432943	0.85[EUR][1000 genomes]
rs2432945	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2432953	0.83[EUR][1000 genomes]
rs2432956	0.80[ASN][1000 genomes]
rs2432957	0.82[ASN][1000 genomes]
rs4335940	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4467261	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4592848	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4664438	0.84[EUR][1000 genomes]
rs6735771	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72860233	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3693426	chr2:151725792-152295862	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1012891	chr2:152019809-152306897	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv1013484	chr2:152028515-152473913	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv535983	chr2:152028515-152473913	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1012139	chr2:152114637-152389516	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv1011339	chr2:152114637-152392940	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv999748	chr2:152135514-152476396	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
8	nsv834418	chr2:152205803-152385516	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5024580	RIF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152261600-152266000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr2:152261800-152265800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:152264000-152265600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr2:152264800-152268000	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr2:152265000-152265400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr2:152265000-152265400	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr2:152265000-152265400	Enhancers	Fetal Muscle Trunk	muscle
8	chr2:152265000-152268600	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr2:152265200-152265800	Enhancers	K562	blood
10	chr2:152265200-152266000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr2:152265200-152266000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr2:152265200-152266200	Weak transcription	Right Atrium	heart

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