Variant report

Variant	rs4294557
Chromosome Location	chr11:5138733-5138734
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	11:5137223-5140360..11:5566274-5571131	Hela-S3	cervix:
2	11:5137223-5140360..11:5505728-5514500	Hela-S3	cervix:
3	11:5137223-5140360..11:5721056-5732713	GM12878	blood:
4	11:5137223-5140360..11:5527719-5533869	GM12878	blood:
5	11:5137223-5140360..11:5533869-5541626	GM12878	blood:
6	chr11:5138048..5140738-chr11:5144465..5146975,2	K562	blood:
7	11:5137223-5140360..11:5243048-5250847	GM12878	blood:
8	chr11:5138070..5140863-chr11:5316692..5319201,2	K562	blood:
9	11:5137223-5140360..11:5714465-5718134	K562	blood:
10	11:5137223-5140360..11:5407716-5412355	GM12878	blood:
11	11:4778081-4789138..11:5137223-5140360	Hela-S3	cervix:
12	11:5137223-5140360..11:5250847-5268367	Hela-S3	cervix:
13	11:5137223-5140360..11:5700314-5707362	H1-hESC	embryonic stem cell:	embryo

No data

Variant related genes	Relation type
ENSG00000244734	Chromatin interaction
ENSG00000184698	Chromatin interaction
ENSG00000260629	Chromatin interaction
ENSG00000221031	Chromatin interaction
ENSG00000181616	Chromatin interaction
ENSG00000175518	Chromatin interaction
ENSG00000132274	Chromatin interaction
ENSG00000167346	Chromatin interaction
ENSG00000181609	Chromatin interaction
ENSG00000205494	Chromatin interaction
ENSG00000132256	Chromatin interaction
ENSG00000223609	Chromatin interaction
ENSG00000175520	Chromatin interaction
ENSG00000229988	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10500616	1.00[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs10500617	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs10768545	0.94[CEU][hapmap];0.88[GIH][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10768550	0.91[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs10768575	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10837295	0.90[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs10837329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10837334	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10837335	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11035684	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11035710	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11035736	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11035740	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11035743	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11035765	1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11035774	0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11530045	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12221996	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12360617	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12364567	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12420900	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1463380	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1463381	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2472527	0.86[JPT][hapmap];0.85[MEX][hapmap]
rs2472530	0.86[JPT][hapmap];0.85[MEX][hapmap]
rs2499948	0.87[CHD][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap]
rs2499949	0.86[JPT][hapmap]
rs2499951	0.86[JPT][hapmap]
rs4278501	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4370933	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[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];1.00[ASN][1000 genomes]
rs4617575	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61880360	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7350513	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7931931	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054847	chr11:4642875-5200656	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	nsv1046693	chr11:4958462-5177455	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
3	nsv540938	chr11:4958462-5177455	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
4	esv2760169	chr11:4961518-5233821	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
5	nsv553219	chr11:5026200-5214413	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
6	nsv896920	chr11:5068137-5221825	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
7	nsv896923	chr11:5091882-5199208	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
8	nsv896924	chr11:5098714-5221825	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
9	nsv553222	chr11:5102476-5151516	ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
10	nsv553223	chr11:5116128-5149332	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
11	nsv467668	chr11:5138733-5207389	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	27 gene(s)	inside rSNPs	diseases
12	nsv553224	chr11:5138733-5207389	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4294557	MRPL23	cis	parietal	SCAN
rs4294557	OR52E2	cis	parietal	SCAN
rs4294557	SYT8	cis	parietal	SCAN
rs4294557	MUC2	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:5137400-5144000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr11:5138600-5139000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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