Variant report

Variant	rs10899397
Chromosome Location	chr11:77361025-77361026
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:77347391..77349326-chr11:77360407..77363376,3	MCF-7	breast:
2	chr11:77348510..77350805-chr11:77358288..77361555,3	K562	blood:
3	chr11:77300520..77303029-chr11:77359483..77361400,2	K562	blood:

Variant related genes	Relation type
ENSG00000074201	Chromatin interaction
ENSG00000178301	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10466710	0.94[CHB][hapmap];0.84[CHD][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs10793257	0.94[CHB][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap]
rs10899396	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10899401	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11237264	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11237279	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12294668	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12418931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1783547	0.85[ASN][1000 genomes]
rs1945747	1.00[CHB][hapmap]
rs2508184	0.87[ASN][1000 genomes]
rs35711367	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[ASN][1000 genomes]
rs4945185	0.80[EUR][1000 genomes]
rs570786	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs584732	0.85[ASN][1000 genomes]
rs585172	0.85[ASN][1000 genomes]
rs585721	0.80[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.83[YRI][hapmap];0.87[ASN][1000 genomes]
rs591283	0.85[ASN][1000 genomes]
rs598933	0.87[ASN][1000 genomes]
rs600968	0.85[ASN][1000 genomes]
rs601551	0.80[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.83[YRI][hapmap];0.87[ASN][1000 genomes]
rs603462	0.85[ASN][1000 genomes]
rs608539	0.85[ASN][1000 genomes]
rs611671	0.85[ASN][1000 genomes]
rs611906	0.85[ASN][1000 genomes]
rs636041	0.85[ASN][1000 genomes]
rs647235	0.85[ASN][1000 genomes]
rs649671	0.86[ASN][1000 genomes]
rs667213	0.85[ASN][1000 genomes]
rs685474	0.85[ASN][1000 genomes]
rs694893	0.85[ASN][1000 genomes]
rs7925289	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048360	chr11:76900813-77387933	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv541089	chr11:76900813-77387933	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1049603	chr11:76900813-77520411	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv541090	chr11:76900813-77520411	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1038974	chr11:77284036-77431228	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv1041384	chr11:77284558-77419809	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv1048892	chr11:77290458-77431228	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv1053074	chr11:77290458-77435831	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
9	nsv468641	chr11:77301341-77420314	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
10	nsv555452	chr11:77301341-77420314	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
11	nsv1035494	chr11:77309696-77431228	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10899397	NDUFC2	cis	cerebellum	SCAN
rs10899397	KCTD14	cis	cerebellum	SCAN
rs10899397	KCTD21	cis	cerebellum	SCAN
rs10899397	C11orf67	cis	cerebellum	SCAN
rs10899397	AQP11	cis	parietal	SCAN
rs10899397	ALG8	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77356000-77361200	Weak transcription	HepG2	liver
2	chr11:77356000-77377800	Weak transcription	Osteobl	bone
3	chr11:77359400-77368600	Weak transcription	HSMMtube	muscle
4	chr11:77360400-77361800	Enhancers	Fetal Intestine Large	intestine
5	chr11:77360400-77419200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr11:77360600-77361200	Enhancers	Fetal Intestine Small	intestine
7	chr11:77361000-77361200	Bivalent Enhancer	Small Intestine	intestine
8	chr11:77361000-77361400	Enhancers	K562	blood

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