Variant report

Variant	rs649460
Chromosome Location	chr11:74197326-74197327
allele	A/C
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	POLR2A	chr11:74197266-74197799	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:74189754..74191906-chr11:74197313..74199883,3	MCF-7	breast:
2	chr11:74196733..74198968-chr11:74202003..74205722,4	K562	blood:
3	chr11:74196620..74198242-chr11:74204138..74205722,2	K562	blood:

Variant related genes	Relation type
ENSG00000254974	TF binding region
ENSG00000175536	Chromatin interaction
ENSG00000254837	Chromatin interaction
ENSG00000077514	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs12364885	0.87[ASN][1000 genomes]
rs1280207	0.91[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs1280211	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1280212	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1280217	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1280220	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1298868	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1315212	0.82[MEX][hapmap]
rs1316182	0.82[MEX][hapmap]
rs1433968	0.80[EUR][1000 genomes]
rs1617968	0.80[EUR][1000 genomes]
rs1655469	0.81[EUR][1000 genomes]
rs1655475	0.81[EUR][1000 genomes]
rs1783201	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1783202	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1787091	0.83[MEX][hapmap]
rs1787097	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1787102	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1787109	0.81[EUR][1000 genomes]
rs2509562	0.83[MEX][hapmap]
rs2509563	0.83[MEX][hapmap]
rs2509993	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2916310	0.80[EUR][1000 genomes]
rs3741128	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3741129	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs581831	0.98[ASN][1000 genomes]
rs583404	0.83[EUR][1000 genomes]
rs586088	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs589161	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs589970	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs594143	0.80[EUR][1000 genomes]
rs594437	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs594628	0.88[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs598525	0.83[EUR][1000 genomes]
rs598821	0.83[EUR][1000 genomes]
rs598926	0.80[EUR][1000 genomes]
rs601419	0.98[ASN][1000 genomes]
rs601904	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs602936	0.81[EUR][1000 genomes]
rs608978	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs610435	0.81[EUR][1000 genomes]
rs615732	0.80[EUR][1000 genomes]
rs617343	0.82[EUR][1000 genomes]
rs617989	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs627824	0.82[EUR][1000 genomes]
rs627886	0.83[EUR][1000 genomes]
rs628574	0.80[EUR][1000 genomes]
rs640094	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs641213	0.88[YRI][hapmap]
rs645269	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs645541	0.83[MEX][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs648677	0.83[MEX][hapmap]
rs654943	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs655025	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs656506	0.92[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs657339	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.98[TSI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6592566	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs659581	0.83[MEX][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs660123	0.82[EUR][1000 genomes]
rs660418	0.82[EUR][1000 genomes]
rs660855	0.83[MEX][hapmap]
rs661781	0.83[MEX][hapmap]
rs663016	0.83[MEX][hapmap]
rs663555	0.83[MEX][hapmap]
rs674306	0.83[MEX][hapmap]
rs675086	0.83[MEX][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs675450	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs676537	0.83[MEX][hapmap]
rs7121457	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7928160	0.80[EUR][1000 genomes]
rs7931184	0.81[EUR][1000 genomes]
rs9787964	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv832209	chr11:74155883-74329119	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv897913	chr11:74171997-74216705	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs649460	SNORD15B	cis	parietal	SCAN
rs649460	ANO1	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74191400-74204000	Weak transcription	Ovary	ovary
2	chr11:74192400-74203200	Weak transcription	Duodenum Mucosa	Duodenum
3	chr11:74193400-74200600	Weak transcription	Primary T cells from cord blood	blood
4	chr11:74195800-74197600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr11:74196000-74197600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr11:74196800-74197600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr11:74196800-74199600	Enhancers	HepG2	liver
8	chr11:74197000-74197600	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr11:74197000-74203800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr11:74197200-74203000	Weak transcription	K562	blood
11	chr11:74197200-74203200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr11:74197200-74204200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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