Variant report

Variant	rs34448818
Chromosome Location	chr3:47841312-47841313
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	RAD21	chr3:47841302-47841565	H1-hESC	embryonic stem cell:	n/a	chr3:47841431-47841450
2	RAD21	chr3:47841255-47841483	SK-N-SH_RA	brain:	n/a	chr3:47841431-47841450
3	KAP1	chr3:47841225-47841418	U2OS	brain:	n/a	n/a
4	CTCF	chr3:47841280-47841530	SK-N-SH_RA	brain:	n/a	chr3:47841428-47841449 chr3:47841433-47841451 chr3:47841434-47841450
5	CTCF	chr3:47841300-47841450	HBMEC	blood vessel:	n/a	chr3:47841428-47841449 chr3:47841434-47841450
6	CTCF	chr3:47841268-47841584	K562	blood:	n/a	chr3:47841428-47841449 chr3:47841433-47841451 chr3:47841434-47841450
7	CTCF	chr3:47841220-47841370	HRPEpiC	eye:	n/a	n/a
8	CTCF	chr3:47841280-47841430	HFF-Myc	foreskin:	n/a	n/a
9	ZNF143	chr3:47841281-47841540	K562	blood:	n/a	n/a
10	TEAD4	chr3:47841156-47841586	H1-hESC	embryonic stem cell:	n/a	n/a
11	CTCF	chr3:47841264-47841625	GM12878	blood:	n/a	chr3:47841428-47841449 chr3:47841433-47841451 chr3:47841434-47841450
12	CTCF	chr3:47841264-47841536	K562	blood:	n/a	chr3:47841428-47841449 chr3:47841433-47841451 chr3:47841434-47841450
13	CTCF	chr3:47841291-47841541	MCF-7	breast:	n/a	chr3:47841428-47841449 chr3:47841433-47841451 chr3:47841434-47841450
14	CTCF	chr3:47841300-47841450	NHDF-neo	bronchial:	n/a	chr3:47841428-47841449 chr3:47841434-47841450
15	CTCF	chr3:47841197-47841649	SK-N-SH	brain:	n/a	chr3:47841428-47841449 chr3:47841433-47841451 chr3:47841434-47841450
16	CTCF	chr3:47841287-47841530	H1-hESC	embryonic stem cell:	n/a	chr3:47841428-47841449 chr3:47841433-47841451 chr3:47841434-47841450
17	CTCF	chr3:47841300-47841450	WI-38	lung:	n/a	chr3:47841428-47841449 chr3:47841434-47841450
18	RAD21	chr3:47841275-47841535	H1-hESC	embryonic stem cell:	n/a	chr3:47841431-47841450
19	CTCF	chr3:47841201-47841588	H1-hESC	embryonic stem cell:	n/a	chr3:47841428-47841449 chr3:47841433-47841451 chr3:47841434-47841450
20	TEAD4	chr3:47841130-47841547	H1-hESC	embryonic stem cell:	n/a	n/a
21	CTCF	chr3:47841257-47841652	K562	blood:	n/a	chr3:47841428-47841449 chr3:47841433-47841451 chr3:47841434-47841450
22	CTCF	chr3:47841260-47841410	HMEC	breast:	n/a	n/a
23	RAD21	chr3:47841214-47841646	H1-hESC	embryonic stem cell:	n/a	chr3:47841431-47841450
24	CTCF	chr3:47841197-47841677	A549	lung:	n/a	chr3:47841428-47841449 chr3:47841433-47841451 chr3:47841434-47841450
25	CTCF	chr3:47841280-47841430	GM12870	blood:	n/a	n/a
26	CTCF	chr3:47841274-47841563	MCF-7	breast:	n/a	chr3:47841428-47841449 chr3:47841433-47841451 chr3:47841434-47841450
27	CTCF	chr3:47841261-47841627	K562	blood:	n/a	chr3:47841428-47841449 chr3:47841433-47841451 chr3:47841434-47841450

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:47839929..47843313-chr3:47843454..47847065,4	MCF-7	breast:
2	chr3:47839468..47842500-chr3:47843007..47845757,4	K562	blood:

Variant related genes	Relation type
DHX30	TF binding region
ENSG00000132153	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 17 )

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

rs_ID	r²[population]
rs1060407	0.81[CEU][hapmap]
rs11707679	0.81[CEU][hapmap]
rs11709289	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11711725	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs11716779	0.82[AMR][1000 genomes]
rs13072132	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17785248	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes]
rs319682	0.81[CEU][hapmap]
rs319696	0.81[CEU][hapmap]
rs34507589	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35012836	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4858871	0.81[CEU][hapmap]
rs5016900	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62260764	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs62262084	0.82[AMR][1000 genomes]
rs6763824	0.92[CEU][hapmap];0.83[GIH][hapmap];0.88[TSI][hapmap]
rs7430913	0.86[CEU][hapmap]
rs777015	0.81[CEU][hapmap]
rs796566	0.84[CEU][hapmap]
rs810334	0.81[CEU][hapmap]

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	nsv1003072	chr3:47673628-47869154	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv876758	chr3:47681881-47842234	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
3	nsv834679	chr3:47749475-47924006	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	167 gene(s)	inside rSNPs	diseases
4	nsv965333	chr3:47815622-47845296	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv10270	chr3:47822606-47845578	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs34448818	ZNF589	cis	Esophagus Muscularis	GTEx
rs34448818	MRPS18AP1	cis	Esophagus Muscularis	GTEx
rs34448818	SMARCC1	Cis_1M	lymphoblastoid	RTeQTL
rs34448818	NME6	cis	Esophagus Muscularis	GTEx
rs34448818	MRPS18AP1	cis	Thyroid	GTEx
rs34448818	ZNF589	cis	cerebellum	SCAN
rs34448818	SMARCC1	cis	cerebellum	SCAN
rs34448818	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs34448818	MRPS18AP1	cis	Nerve Tibial	GTEx
rs34448818	CDC25A	cis	Muscle Skeletal	GTEx
rs34448818	ZNF589	cis	Nerve Tibial	GTEx
rs34448818	ZNF589	cis	Artery Tibial	GTEx
rs34448818	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs34448818	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs34448818	ZNF589	cis	parietal	SCAN
rs34448818	CDC25A	cis	cerebellum	SCAN
rs34448818	MRPS18AP1	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47831200-47842800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr3:47833600-47843600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:47839200-47843000	Weak transcription	K562	blood
4	chr3:47839200-47843200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:47839600-47843400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr3:47839800-47843400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:47840200-47841800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:47840400-47842600	Weak transcription	HepG2	liver
9	chr3:47840600-47843400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:47840800-47843800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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