Variant report

Variant	rs916512
Chromosome Location	chr3:120144064-120144065
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:120143073..120145920-chr3:120273306..120275738,2	MCF-7	breast:
2	chr3:120142587..120145112-chr3:120167743..120170457,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163430	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1147682	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1147683	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1147686	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1147687	0.83[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1147691	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1147692	0.83[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1147702	0.87[JPT][hapmap]
rs1147704	0.95[CEU][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1147705	0.87[JPT][hapmap]
rs1259290	0.82[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1259291	0.82[ASN][1000 genomes]
rs1259292	0.82[ASN][1000 genomes]
rs1259293	0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs1259294	0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs1259295	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1259296	0.82[ASN][1000 genomes]
rs1259297	1.00[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1259327	0.96[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1588890	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1588891	0.81[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1606872	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1606873	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1615793	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs1621291	0.83[CEU][hapmap]
rs1623323	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1716840	0.83[CEU][hapmap]
rs1716846	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1733325	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1733327	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1733329	0.82[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1733331	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1733353	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1733354	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2673704	1.00[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2700260	0.85[CHB][hapmap];0.94[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2702156	0.83[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2702158	0.82[CEU][hapmap]
rs2702164	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2943754	0.82[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6438576	1.00[YRI][hapmap]
rs6438578	1.00[YRI][hapmap]
rs787197	1.00[YRI][hapmap]
rs916509	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs916510	0.85[ASN][1000 genomes]
rs916511	0.83[ASN][1000 genomes]
rs939500	0.88[JPT][hapmap]
rs950649	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs950650	0.86[AFR][1000 genomes];0.87[AMR][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	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	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
3	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
4	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
5	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
6	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
7	esv3369381	chr3:120066425-120425510	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	esv3350409	chr3:120066445-120425480	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120115800-120151000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:120135400-120151600	Genic enhancers	Osteobl	bone
3	chr3:120136800-120145200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:120136800-120147400	Enhancers	Duodenum Smooth Muscle	Duodenum
5	chr3:120136800-120147600	Enhancers	Adipose Nuclei	Adipose
6	chr3:120136800-120148400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr3:120136800-120148600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr3:120137000-120149600	Enhancers	Rectal Smooth Muscle	rectum
9	chr3:120137400-120162200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr3:120137800-120161600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:120138200-120145400	Weak transcription	NHEK	skin
12	chr3:120138200-120146400	Weak transcription	Fetal Intestine Large	intestine
13	chr3:120138200-120154200	Weak transcription	HMEC	breast
14	chr3:120138200-120157200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:120138200-120162000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr3:120138200-120167800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr3:120138200-120169200	Weak transcription	Gastric	stomach
18	chr3:120138400-120148600	Genic enhancers	NHDF-Ad	bronchial
19	chr3:120138400-120155600	Weak transcription	Esophagus	oesophagus
20	chr3:120138600-120147800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr3:120138600-120148600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr3:120138800-120150600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr3:120139000-120148000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr3:120139200-120145000	Weak transcription	Liver	Liver
25	chr3:120140600-120145000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:120140800-120144200	Weak transcription	Fetal Intestine Small	intestine
27	chr3:120140800-120145000	Weak transcription	Brain Substantia Nigra	brain
28	chr3:120140800-120147600	Strong transcription	HSMM	muscle
29	chr3:120140800-120154200	Weak transcription	Psoas Muscle	Psoas
30	chr3:120141000-120144200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr3:120141000-120144200	Weak transcription	Fetal Kidney	kidney
32	chr3:120141000-120144400	Strong transcription	Muscle Satellite Cultured Cells	--
33	chr3:120141000-120145800	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr3:120141200-120145400	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr3:120141200-120147800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr3:120141200-120150800	Weak transcription	Brain Angular Gyrus	brain
37	chr3:120141400-120146600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr3:120141600-120145200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr3:120142000-120144200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr3:120142000-120144200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr3:120142000-120144400	Enhancers	Right Atrium	heart
42	chr3:120142000-120144600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr3:120142000-120144600	Strong transcription	Placenta	Placenta
44	chr3:120142000-120146800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:120142000-120148200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr3:120142000-120148600	Enhancers	Aorta	Aorta
47	chr3:120142000-120149400	Genic enhancers	Fetal Stomach	stomach
48	chr3:120142000-120153600	Genic enhancers	NHLF	lung
49	chr3:120142200-120144200	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr3:120142400-120145000	Weak transcription	Lung	lung

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