Variant report

Variant	rs4944947
Chromosome Location	chr11:74445699-74445700
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	REST	chr11:74445640-74445948	SK-N-SH	brain:	n/a	n/a
2	REST	chr11:74445617-74445915	PFSK-1	brain:	n/a	n/a
3	REST	chr11:74445697-74445833	Hela-S3	cervix:	n/a	n/a
4	REST	chr11:74445628-74445972	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:74443489..74448156-chr11:74456515..74460463,6	K562	blood:
2	chr11:74438602..74440295-chr11:74445038..74446669,2	K562	blood:
3	chr11:74440192..74442895-chr11:74445109..74448883,3	MCF-7	breast:

Variant related genes	Relation type
CHRDL2	TF binding region
ENSG00000054938	Chromatin interaction
ENSG00000227615	Chromatin interaction
ENSG00000166439	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10751241	0.82[JPT][hapmap]
rs10899041	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10899042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11236234	0.82[ASN][1000 genomes]
rs11236236	0.91[CHD][hapmap];0.86[ASN][1000 genomes]
rs11236244	0.81[ASN][1000 genomes]
rs12221841	0.82[JPT][hapmap]
rs12223076	0.97[ASN][1000 genomes]
rs12223417	0.91[CHB][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs12417156	0.91[CHD][hapmap]
rs12419197	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12421899	0.83[ASN][1000 genomes]
rs12576129	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs12576444	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1433771	0.96[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17133461	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs2298746	0.81[CHD][hapmap];0.82[JPT][hapmap]
rs2304683	0.82[JPT][hapmap]
rs3814726	0.84[CHD][hapmap];0.82[JPT][hapmap]
rs4483614	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs4944061	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs4944944	0.85[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4944950	0.88[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs4944960	0.82[JPT][hapmap]
rs4944961	0.81[CHD][hapmap];0.82[JPT][hapmap]
rs61734374	0.83[ASN][1000 genomes]
rs61897000	0.86[ASN][1000 genomes]
rs6592594	0.96[ASN][1000 genomes]
rs7103136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7105085	0.81[CHD][hapmap];0.82[JPT][hapmap]
rs7128739	0.81[CHD][hapmap];0.81[JPT][hapmap]
rs919877	0.82[JPT][hapmap]
rs968305	0.91[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757451	chr11:73842609-74545888	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	esv2759837	chr11:73842609-74557597	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	esv34979	chr11:73878688-74533452	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2758277	chr11:73887567-74557597	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv825994	chr11:73936667-74534455	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
6	nsv932190	chr11:74359867-74618935	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs4944947	XRRA1	cis	Esophagus Mucosa	GTEx
rs4944947	NEU3	cis	cerebellum	SCAN
rs4944947	RP11-147I3.1	cis	Thyroid	GTEx
rs4944947	XRRA1	cis	Muscle Skeletal	GTEx
rs4944947	XRRA1	cis	cerebellum	SCAN
rs4944947	XRRA1	cis	Thyroid	GTEx
rs4944947	PAAF1	cis	parietal	SCAN
rs4944947	XRRA1	cis	multi-tissue	Pritchard
rs4944947	XRRA1	cis	Skin Sun Exposed Lower leg	GTEx
rs4944947	XRRA1	cis	lymphoblastoid	seeQTL
rs4944947	XRRA1	cis	parietal	SCAN
rs4944947	XRRA1	cis	Esophagus Muscularis	GTEx
rs4944947	XRRA1	cis	Artery Tibial	GTEx
rs4944947	XRRA1	cis	Whole Blood	GTEx
rs4944947	XRRA1	Cis_1M	lymphoblastoid	RTeQTL
rs4944947	XRRA1	cis	Adipose Subcutaneous	GTEx
rs4944947	KRTAP5-11	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74443400-74446200	Weak transcription	Spleen	Spleen
2	chr11:74445400-74446200	Bivalent Enhancer	Fetal Muscle Leg	muscle
3	chr11:74445400-74447800	Enhancers	HepG2	liver
4	chr11:74445600-74445800	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr11:74445600-74459000	Weak transcription	A549	lung

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