Variant report

Variant	rs3858449
Chromosome Location	chr11:32453536-32453537
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	JUN	chr11:32453532-32456818	K562	blood:	n/a	chr11:32453717-32453725
2	POLR2A	chr11:32453512-32457942	NB4	blood:	n/a	n/a
3	POLR2A	chr11:32453286-32457646	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:32453512..32456485-chr11:32618384..32621260,2	K562	blood:

Variant related genes	Relation type
WT1	TF binding region
WT1-AS	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10835913	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10835914	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10835915	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10835917	0.84[CHB][hapmap];0.93[CHD][hapmap]
rs11031778	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11031787	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11031788	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12575247	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1569776	0.91[MEX][hapmap]
rs1799925	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2234585	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2301250	0.83[CHD][hapmap]
rs2418910	0.83[CHD][hapmap]
rs2900741	0.85[CHD][hapmap]
rs2900753	0.82[EUR][1000 genomes]
rs34163689	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3809060	0.81[CHD][hapmap]
rs3809061	0.81[CHD][hapmap]
rs3858451	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3930513	0.81[CHD][hapmap]
rs5030141	1.00[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];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5030171	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5030277	0.86[MEX][hapmap]
rs5030280	0.86[MEX][hapmap]
rs5030281	0.86[MEX][hapmap]
rs59518979	0.85[EUR][1000 genomes]
rs61889255	0.85[EUR][1000 genomes]
rs61889256	0.84[EUR][1000 genomes]
rs7110547	0.81[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832108	chr11:32395937-32560583	Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1044547	chr11:32435753-32465233	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv2753303	chr11:32447324-32494924	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1051559	chr11:32447347-32465233	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3858449	CSTF3	cis	cerebellum	SCAN
rs3858449	CRYGA	trans	parietal	SCAN
rs3858449	MTMR4	trans	cerebellum	SCAN
rs3858449	PRR5L	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:32448800-32454800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
2	chr11:32450200-32457400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
3	chr11:32452200-32454400	Active TSS	Fetal Kidney	kidney
4	chr11:32452600-32454200	Flanking Active TSS	Ovary	ovary
5	chr11:32452800-32453600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
6	chr11:32452800-32454400	Weak transcription	Pancreas	Pancrea
7	chr11:32452800-32454800	Weak transcription	Gastric	stomach
8	chr11:32453000-32453600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr11:32453200-32453800	Enhancers	K562	blood
10	chr11:32453400-32453600	Bivalent/Poised TSS	Right Ventricle	heart
11	chr11:32453400-32459600	Active TSS	Right Atrium	heart

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