Variant report

Variant	rs12158983
Chromosome Location	chr22:32748873-32748874
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr22:32748871-32748991	H1-hESC	embryonic stem cell:	n/a	n/a
2	RAD21	chr22:32748839-32749050	H1-hESC	embryonic stem cell:	n/a	n/a
3	RAD21	chr22:32748703-32749119	H1-hESC	embryonic stem cell:	n/a	chr22:32749053-32749072

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	22:32360288-32405313..22:32740683-32750950	K562	blood:
2	22:32665993-32670527..22:32740683-32750950	H1-hESC	embryonic stem cell:	embryo
3	22:32513817-32522138..22:32740683-32750950	K562	blood:
4	22:32740683-32750950..22:32846948-32860159	K562	blood:
5	22:32529813-32538538..22:32740683-32750950	H1-hESC	embryonic stem cell:	embryo
6	22:31936958-31958600..22:32740683-32750950	Hela-S3	cervix:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RFPL3-AS1-4	chr22:32748825-32749001	NONHSAT084957

No data

Variant related genes	Relation type
RFPL3	TF binding region
ENSG00000230866	Chromatin interaction
ENSG00000224050	Chromatin interaction
ENSG00000234479	Chromatin interaction
ENSG00000184459	Chromatin interaction
ENSG00000240647	Chromatin interaction
ENSG00000239674	Chromatin interaction
ENSG00000232707	Chromatin interaction
ENSG00000214093	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs12160488	0.87[ASN][1000 genomes]
rs12484018	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12484101	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12484208	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs28625291	0.87[ASN][1000 genomes]
rs34757928	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs58713361	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5994553	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5994554	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5994555	0.87[ASN][1000 genomes]
rs5994556	0.87[ASN][1000 genomes]
rs5994557	0.87[ASN][1000 genomes]
rs5994558	0.87[ASN][1000 genomes]
rs5994559	0.87[ASN][1000 genomes]
rs5998433	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5998435	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5998442	0.87[ASN][1000 genomes]
rs5998443	0.87[ASN][1000 genomes]
rs5998444	0.87[ASN][1000 genomes]
rs5998445	0.87[ASN][1000 genomes]
rs5998449	0.87[ASN][1000 genomes]
rs5998450	0.87[ASN][1000 genomes]
rs5998452	0.87[ASN][1000 genomes]
rs5998454	0.87[ASN][1000 genomes]
rs5998455	0.87[ASN][1000 genomes]
rs5998458	0.87[ASN][1000 genomes]
rs5998460	0.87[ASN][1000 genomes]
rs5998462	0.87[ASN][1000 genomes]
rs5998464	0.87[ASN][1000 genomes]
rs5998465	0.87[ASN][1000 genomes]
rs5998466	0.87[ASN][1000 genomes]
rs5998467	0.87[ASN][1000 genomes]
rs61644931	0.87[ASN][1000 genomes]
rs713647	0.87[ASN][1000 genomes]
rs7285060	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73166371	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs73166382	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs73166395	0.80[AMR][1000 genomes]
rs73881641	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73881643	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73881644	0.87[ASN][1000 genomes]
rs8139945	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948789	chr22:32462505-32764760	Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1065175	chr22:32467617-32761093	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv544680	chr22:32467617-32761093	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	esv2830423	chr22:32477718-32767825	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	esv2422247	chr22:32486448-32788258	Strong transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
6	nsv459874	chr22:32574274-32866934	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
7	nsv588895	chr22:32574274-32866934	Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
8	nsv1064737	chr22:32603912-32829725	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
9	nsv964624	chr22:32740318-32751906	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:32740200-32752000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr22:32741800-32750200	Weak transcription	Right Atrium	heart
3	chr22:32742400-32750200	Weak transcription	HUVEC	blood vessel
4	chr22:32746400-32751000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr22:32747200-32750400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr22:32748400-32751000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr22:32748600-32749400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr22:32748600-32749600	Enhancers	Lung	lung
9	chr22:32748800-32750200	Enhancers	Spleen	Spleen
10	chr22:32748800-32752000	Weak transcription	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links