Variant report

Variant	rs1085612
Chromosome Location	chr3:120033459-120033460
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:120032416..120034924-chr3:120037587..120040555,3	MCF-7	breast:

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1085613	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1085625	0.81[JPT][hapmap]
rs1092829	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1147682	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1147683	0.84[AFR][1000 genomes]
rs1147686	0.84[AFR][1000 genomes]
rs1147687	0.80[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs1147691	0.84[AFR][1000 genomes]
rs1147692	0.86[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs1147704	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs11554681	0.84[JPT][hapmap]
rs1259290	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1259295	1.00[YRI][hapmap]
rs1259297	1.00[YRI][hapmap]
rs1259327	1.00[YRI][hapmap]
rs12638445	0.86[ASN][1000 genomes]
rs13075278	0.84[JPT][hapmap]
rs13100050	0.84[JPT][hapmap]
rs1356112	0.80[CHB][hapmap]
rs1515574	0.83[JPT][hapmap]
rs1515576	0.93[ASN][1000 genomes]
rs1588890	0.84[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs1588891	0.83[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs1606872	0.80[AFR][1000 genomes]
rs1606873	0.84[AFR][1000 genomes]
rs1615793	0.84[AFR][1000 genomes]
rs1621291	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs1623323	0.84[AFR][1000 genomes]
rs1716839	0.80[CHB][hapmap]
rs1716840	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs1716846	0.84[AFR][1000 genomes]
rs1733325	0.84[AFR][1000 genomes]
rs1733327	0.84[AFR][1000 genomes]
rs1733329	0.86[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs1733331	0.84[AFR][1000 genomes]
rs1733353	0.84[AFR][1000 genomes]
rs1733354	0.84[AFR][1000 genomes]
rs1849933	0.81[EUR][1000 genomes]
rs2030413	0.81[ASN][1000 genomes]
rs2138259	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2638592	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2673704	1.00[YRI][hapmap]
rs2702156	0.86[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs2702164	0.84[AFR][1000 genomes]
rs2943754	0.86[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs3914498	0.81[JPT][hapmap]
rs6438576	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6438578	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6438579	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7622363	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs787197	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs787199	0.89[ASN][1000 genomes]
rs787201	0.93[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs787202	0.80[EUR][1000 genomes]
rs787210	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs805080	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs810888	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs813698	0.82[ASN][1000 genomes]
rs916509	1.00[YRI][hapmap]
rs916512	1.00[YRI][hapmap]
rs939499	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs950649	0.84[AFR][1000 genomes]
rs950650	0.84[AFR][1000 genomes]
rs9851825	0.86[CHB][hapmap];0.88[JPT][hapmap];0.89[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	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv877376	chr3:119824037-120119446	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv829698	chr3:119960869-120129126	Enhancers Strong transcription Flanking Active TSS Active TSS Weak 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 miRNA target site	24 gene(s)	inside rSNPs	diseases
8	nsv1012127	chr3:120015620-120272893	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active 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 miRNA target site	26 gene(s)	inside rSNPs	diseases
9	nsv536707	chr3:120015620-120272893	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
11	esv3372733	chr3:120030562-120034960	Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
12	esv3324373	chr3:120031312-120034110	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	n/a

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120024400-120049200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:120025400-120040600	Weak transcription	Fetal Lung	lung
3	chr3:120026600-120042400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:120026600-120060800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:120026800-120049200	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr3:120026800-120067200	Weak transcription	Aorta	Aorta
7	chr3:120030000-120042600	Weak transcription	HMEC	breast
8	chr3:120030600-120034200	Weak transcription	Adipose Nuclei	Adipose
9	chr3:120031000-120041200	Weak transcription	Fetal Stomach	stomach
10	chr3:120031000-120042400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr3:120031000-120055600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:120031200-120033800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:120031400-120040600	Weak transcription	Ovary	ovary
14	chr3:120031400-120042400	Weak transcription	A549	lung
15	chr3:120031600-120034600	Weak transcription	Fetal Muscle Leg	muscle
16	chr3:120031800-120033800	Weak transcription	Esophagus	oesophagus
17	chr3:120031800-120034400	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr3:120032200-120034200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:120032400-120047600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:120032600-120033600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr3:120032800-120034200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr3:120032800-120042400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr3:120033000-120042200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr3:120033000-120042800	Weak transcription	Brain Hippocampus Middle	brain
25	chr3:120033200-120034800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr3:120033200-120035000	Weak transcription	Primary T cells from cord blood	blood
27	chr3:120033200-120044400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr3:120033200-120050000	Weak transcription	Spleen	Spleen
29	chr3:120033200-120060400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr3:120033200-120060400	Weak transcription	Pancreas	Pancrea
31	chr3:120033200-120067000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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