Variant report

Variant	rs601904
Chromosome Location	chr11:74200739-74200740
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	POLR2A	chr11:74200068-74201122	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:74172990..74175155-chr11:74199456..74202165,2	K562	blood:
2	chr11:74199497..74201596-chr11:74201884..74204811,3	K562	blood:

Variant related genes	Relation type
ENSG00000254837	TF binding region
ENSG00000254974	TF binding region
POLD3	TF binding region
ENSG00000175538	Chromatin interaction
ENSG00000254837	Chromatin interaction
ENSG00000175536	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10736800	0.82[EUR][1000 genomes]
rs12364885	0.85[ASN][1000 genomes]
rs1280207	0.87[MEX][hapmap];0.80[EUR][1000 genomes]
rs1280211	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1280212	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1280217	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1280220	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1298868	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1315199	0.81[EUR][1000 genomes]
rs1315212	0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs1315213	0.82[EUR][1000 genomes]
rs1315214	0.82[EUR][1000 genomes]
rs1315218	0.82[EUR][1000 genomes]
rs1316182	0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs1433968	0.83[EUR][1000 genomes]
rs1610546	0.82[EUR][1000 genomes]
rs1616179	0.82[EUR][1000 genomes]
rs1617788	0.82[EUR][1000 genomes]
rs1617968	0.83[EUR][1000 genomes]
rs1655469	0.83[EUR][1000 genomes]
rs1655475	0.84[EUR][1000 genomes]
rs1783196	0.82[EUR][1000 genomes]
rs1783197	0.82[EUR][1000 genomes]
rs1783201	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1783202	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1787091	0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs1787096	0.81[EUR][1000 genomes]
rs1787097	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1787102	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1787109	0.84[EUR][1000 genomes]
rs1791491	0.81[EUR][1000 genomes]
rs1791492	0.82[EUR][1000 genomes]
rs2509562	0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs2509563	0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs2509993	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2570616	0.82[EUR][1000 genomes]
rs2916310	0.83[EUR][1000 genomes]
rs3017114	0.82[EUR][1000 genomes]
rs3741128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3741129	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs581831	0.95[ASN][1000 genomes]
rs583404	0.80[EUR][1000 genomes]
rs586088	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs589161	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs589970	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs594143	0.83[EUR][1000 genomes]
rs594437	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs594628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs598395	0.82[EUR][1000 genomes]
rs598525	0.81[EUR][1000 genomes]
rs598821	0.80[EUR][1000 genomes]
rs598926	0.83[EUR][1000 genomes]
rs601419	0.95[ASN][1000 genomes]
rs602500	0.81[EUR][1000 genomes]
rs602936	0.83[EUR][1000 genomes]
rs608978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs615732	0.83[EUR][1000 genomes]
rs617343	0.85[EUR][1000 genomes]
rs617989	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs627886	0.80[EUR][1000 genomes]
rs628574	0.83[EUR][1000 genomes]
rs628656	0.80[EUR][1000 genomes]
rs640094	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs642932	0.82[EUR][1000 genomes]
rs645269	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs648677	0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs649460	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]
rs654943	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs655025	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs656506	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs657339	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6592566	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs660057	0.80[EUR][1000 genomes]
rs660107	0.82[EUR][1000 genomes]
rs660855	0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs661781	0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs663016	0.82[EUR][1000 genomes]
rs663499	0.82[EUR][1000 genomes]
rs663555	0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs674306	0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs674660	0.82[EUR][1000 genomes]
rs675450	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs675580	0.82[EUR][1000 genomes]
rs676537	0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs677491	0.82[EUR][1000 genomes]
rs694606	0.82[EUR][1000 genomes]
rs7121457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7928160	0.83[EUR][1000 genomes]
rs7931184	0.84[EUR][1000 genomes]
rs9787964	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	nsv555444	chr11:74200739-74221170	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs601904	UCP2	cis	parietal	SCAN
rs601904	MGC12965	cis	multi-tissue	Pritchard

Chromatin state (count:31 , 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	chr11:74197000-74203800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr11:74197200-74203000	Weak transcription	K562	blood
5	chr11:74197200-74203200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr11:74197200-74204200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr11:74197600-74203200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr11:74197600-74203200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr11:74197600-74203200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr11:74197600-74204000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr11:74197800-74202800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr11:74198200-74203400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr11:74198200-74204000	Weak transcription	Lung	lung
14	chr11:74198200-74204000	Weak transcription	Pancreas	Pancrea
15	chr11:74198400-74203200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr11:74198400-74204000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr11:74198800-74203200	Weak transcription	Brain Anterior Caudate	brain
18	chr11:74199000-74203200	Weak transcription	Placenta	Placenta
19	chr11:74199600-74202200	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr11:74199600-74204000	Weak transcription	HepG2	liver
21	chr11:74200000-74202000	Weak transcription	Liver	Liver
22	chr11:74200000-74203400	Weak transcription	Fetal Intestine Large	intestine
23	chr11:74200200-74203200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr11:74200400-74201800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr11:74200400-74203200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr11:74200400-74203200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr11:74200400-74204200	Weak transcription	Spleen	Spleen
28	chr11:74200600-74202200	Strong transcription	Primary T cells from cord blood	blood
29	chr11:74200600-74203200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr11:74200600-74203200	Weak transcription	HUVEC	blood vessel
31	chr11:74200600-74204000	Weak transcription	Brain Cingulate Gyrus	brain

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