Variant report

Variant	rs9990622
Chromosome Location	chr4:133045796-133045797
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RELA	chr4:133045372-133045804	GM18951	blood:	n/a	n/a
2	WRNIP1	chr4:133044912-133046046	GM12878	blood:	n/a	n/a
3	MXI1	chr4:133045204-133045845	GM12878	blood:	n/a	n/a
4	GTF2F1	chr4:133045694-133045813	H1-hESC	embryonic stem cell:	n/a	n/a
5	RELA	chr4:133045150-133045856	GM12878	blood:	n/a	n/a
6	RUNX3	chr4:133045078-133045814	GM12878	blood:	n/a	n/a
7	RELA	chr4:133045247-133045874	GM19099	blood:	n/a	n/a
8	RUNX3	chr4:133045174-133045823	GM12878	blood:	n/a	n/a
9	NFIC	chr4:133045069-133045813	GM12878	blood:	n/a	n/a
10	JUND	chr4:133045370-133045981	H1-hESC	embryonic stem cell:	n/a	n/a
11	RELA	chr4:133045084-133046021	GM12891	blood:	n/a	n/a
12	USF1	chr4:133045570-133045829	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
ENSG00000251598	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10009200	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10019344	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10033560	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10461212	0.85[AFR][1000 genomes]
rs11723078	0.89[AFR][1000 genomes]
rs11930158	0.90[ASN][1000 genomes]
rs13107581	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13117543	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13124410	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13127678	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13137404	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13141865	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13152802	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1505407	0.86[AFR][1000 genomes]
rs17047796	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1827740	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59368900	0.93[ASN][1000 genomes]
rs6831144	0.83[AMR][1000 genomes]
rs6831366	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6847338	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7660282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7660499	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7661243	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7661355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7666320	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7680111	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7680265	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9790555	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9995917	0.86[AFR][1000 genomes]
rs9996530	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879990	chr4:132783846-133045796	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv879997	chr4:132880203-133045796	Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv470073	chr4:132902055-133101094	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1031888	chr4:132903485-133355824	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv595444	chr4:132937315-133045796	ZNF genes & repeats Enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv880002	chr4:132970231-133082999	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv595445	chr4:133022641-133338765	Weak transcription Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:133045000-133046200	Enhancers	HUES64 Cell Line	embryonic stem cell
2	chr4:133045200-133046000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr4:133045200-133046000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr4:133045200-133046000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:133045200-133046000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr4:133045400-133047800	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr4:133045400-133050000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr4:133045600-133045800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr4:133045600-133045800	Flanking Active TSS	GM12878-XiMat	blood
10	chr4:133045600-133046000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr4:133045600-133046000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
12	chr4:133045600-133046000	Flanking Active TSS	H9 Cell Line	embryonic stem cell
13	chr4:133045600-133046200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr4:133045600-133046200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr4:133045600-133046400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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