Variant report

Variant	rs3741128
Chromosome Location	chr11:74203004-74203005
allele	C/T
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	chr11:74202906-74203020	HepG2	liver:	n/a	n/a
2	POLR2A	chr11:74202461-74203061	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:74200976..74203933-chr11:74257256..74259577,2	MCF-7	breast:
2	chr11:74175411..74179003-chr11:74201966..74206100,6	MCF-7	breast:
3	chr11:74202987..74205917-chr11:75525143..75527102,2	MCF-7	breast:
4	chr11:74196733..74198968-chr11:74202003..74205722,4	K562	blood:
5	chr11:74185351..74193647-chr11:74202565..74206845,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254837	TF binding region
POLD3	TF binding region
ENSG00000175538	Chromatin interaction
ENSG00000254974	Chromatin interaction
ENSG00000198382	Chromatin interaction
ENSG00000255507	Chromatin interaction
ENSG00000255444	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10736800	0.82[EUR][1000 genomes]
rs12364885	0.84[ASN][1000 genomes]
rs1280207	0.96[MEX][hapmap];0.81[EUR][1000 genomes]
rs1280211	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1280212	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1280217	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1280220	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1298868	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1315199	0.82[EUR][1000 genomes]
rs1315212	0.87[MEX][hapmap];0.84[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	0.87[MEX][hapmap];0.84[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	0.84[EUR][1000 genomes]
rs1655475	0.84[EUR][1000 genomes]
rs1783196	0.83[EUR][1000 genomes]
rs1783197	0.83[EUR][1000 genomes]
rs1783201	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1783202	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1787091	0.88[MEX][hapmap];0.84[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];0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1787102	0.94[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1787109	0.84[EUR][1000 genomes]
rs1791491	0.82[EUR][1000 genomes]
rs1791492	0.82[EUR][1000 genomes]
rs2509562	0.88[MEX][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs2509563	0.88[MEX][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs2509993	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2570616	0.83[EUR][1000 genomes]
rs2916310	0.83[EUR][1000 genomes]
rs3017113	0.80[EUR][1000 genomes]
rs3017114	0.82[EUR][1000 genomes]
rs3741129	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs581831	0.95[ASN][1000 genomes]
rs583404	0.81[EUR][1000 genomes]
rs586088	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs589161	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs589970	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs594143	0.83[EUR][1000 genomes]
rs594437	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs594628	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs598395	0.82[EUR][1000 genomes]
rs598525	0.81[EUR][1000 genomes]
rs598821	0.81[EUR][1000 genomes]
rs598926	0.83[EUR][1000 genomes]
rs601419	0.95[ASN][1000 genomes]
rs601904	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]
rs602500	0.81[EUR][1000 genomes]
rs602936	0.84[EUR][1000 genomes]
rs608978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs615732	0.83[EUR][1000 genomes]
rs617343	0.85[EUR][1000 genomes]
rs617989	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs627886	0.81[EUR][1000 genomes]
rs628574	0.83[EUR][1000 genomes]
rs628656	0.81[EUR][1000 genomes]
rs640094	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs641213	0.84[YRI][hapmap]
rs642932	0.82[EUR][1000 genomes]
rs645269	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs645541	0.88[MEX][hapmap]
rs648677	0.88[MEX][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs649460	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]
rs654943	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs655025	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs656506	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs657339	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6592566	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs659581	0.88[MEX][hapmap]
rs660057	0.81[EUR][1000 genomes]
rs660107	0.82[EUR][1000 genomes]
rs660418	0.80[EUR][1000 genomes]
rs660855	0.88[MEX][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs661781	0.88[MEX][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs663016	0.88[MEX][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs663499	0.82[EUR][1000 genomes]
rs663555	0.88[MEX][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs674306	0.88[MEX][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs674660	0.82[EUR][1000 genomes]
rs675086	0.88[MEX][hapmap]
rs675450	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs675580	0.82[EUR][1000 genomes]
rs676537	0.88[MEX][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs677491	0.83[EUR][1000 genomes]
rs694606	0.82[EUR][1000 genomes]
rs7121457	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[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]
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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3741128	UCP2	cis	parietal	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

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	chr11:74197200-74203200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr11:74197200-74204200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr11:74197600-74203200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr11:74197600-74203200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr11:74197600-74203200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr11:74197600-74204000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr11:74198200-74203400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr11:74198200-74204000	Weak transcription	Lung	lung
12	chr11:74198200-74204000	Weak transcription	Pancreas	Pancrea
13	chr11:74198400-74203200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr11:74198400-74204000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr11:74198800-74203200	Weak transcription	Brain Anterior Caudate	brain
16	chr11:74199000-74203200	Weak transcription	Placenta	Placenta
17	chr11:74199600-74204000	Weak transcription	HepG2	liver
18	chr11:74200000-74203400	Weak transcription	Fetal Intestine Large	intestine
19	chr11:74200200-74203200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr11:74200400-74203200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr11:74200400-74203200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr11:74200400-74204200	Weak transcription	Spleen	Spleen
23	chr11:74200600-74203200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr11:74200600-74203200	Weak transcription	HUVEC	blood vessel
25	chr11:74200600-74204000	Weak transcription	Brain Cingulate Gyrus	brain
26	chr11:74200800-74203400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr11:74200800-74203800	Weak transcription	Psoas Muscle	Psoas
28	chr11:74200800-74204000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr11:74201000-74203400	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr11:74201000-74203400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr11:74201000-74204000	Weak transcription	Aorta	Aorta
32	chr11:74201200-74204000	Weak transcription	Right Atrium	heart
33	chr11:74201200-74204200	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr11:74201600-74203400	Weak transcription	Fetal Kidney	kidney
35	chr11:74201600-74203800	Weak transcription	Right Ventricle	heart
36	chr11:74201600-74204000	Weak transcription	Brain Angular Gyrus	brain
37	chr11:74201800-74203200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr11:74201800-74204000	Weak transcription	Osteobl	bone
39	chr11:74202000-74203200	Strong transcription	Liver	Liver
40	chr11:74202000-74203600	Weak transcription	Brain Hippocampus Middle	brain
41	chr11:74202200-74204000	Weak transcription	Primary T cells from cord blood	blood
42	chr11:74202200-74204000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr11:74202200-74204000	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr11:74202400-74203800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr11:74202800-74203200	Strong transcription	Skeletal Muscle Male	skeletal muscle
46	chr11:74202800-74203600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr11:74202800-74203800	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr11:74203000-74203200	Enhancers	Fetal Heart	heart
49	chr11:74203000-74203200	Weak transcription	Fetal Intestine Small	intestine
50	chr11:74203000-74203200	Weak transcription	Sigmoid Colon	Sigmoid Colon

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