Variant report

Variant	rs1259297
Chromosome Location	chr3:120141209-120141210
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	chr3:120140370..120142794-chr3:120168186..120170876,2	MCF-7	breast:
2	chr3:120139169..120141302-chr3:120275834..120278046,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163430	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1147682	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1147683	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1147686	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1147687	0.82[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1147691	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1147692	0.82[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1147702	0.81[CHD][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs1147704	1.00[ASW][hapmap];0.95[CEU][hapmap];0.92[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1147705	0.96[CHD][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs1259290	0.82[ASW][hapmap];0.82[CEU][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1259291	0.89[ASN][1000 genomes]
rs1259292	0.89[ASN][1000 genomes]
rs1259293	1.00[CHD][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs1259294	0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs1259295	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1259296	0.89[ASN][1000 genomes]
rs1259327	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1588890	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1588891	0.81[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1606872	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1606873	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1615793	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs1621291	0.82[CEU][hapmap]
rs1623323	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1716840	0.82[CEU][hapmap]
rs1716846	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1733325	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1733327	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1733329	1.00[ASW][hapmap];0.82[CEU][hapmap];0.87[GIH][hapmap];0.87[MEX][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1733331	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1733353	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1733354	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2138259	0.81[AFR][1000 genomes]
rs2673704	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2700260	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2702156	0.82[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2702158	0.82[CEU][hapmap];0.80[JPT][hapmap];0.81[MKK][hapmap]
rs2702164	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2943754	1.00[ASW][hapmap];0.82[CEU][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6438576	1.00[ASW][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs6438578	1.00[ASW][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs6438579	0.81[AFR][1000 genomes]
rs787197	1.00[YRI][hapmap]
rs916509	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs916512	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]
rs939499	0.81[AFR][1000 genomes]
rs939500	0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs950649	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs950650	0.91[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:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120114400-120143200	Weak transcription	Small Intestine	intestine
2	chr3:120115800-120151000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:120135400-120151600	Genic enhancers	Osteobl	bone
4	chr3:120135600-120141600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:120136800-120141600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:120136800-120141800	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr3:120136800-120141800	Enhancers	Fetal Heart	heart
8	chr3:120136800-120142200	Enhancers	Colon Smooth Muscle	Colon
9	chr3:120136800-120142600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:120136800-120145200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:120136800-120147400	Enhancers	Duodenum Smooth Muscle	Duodenum
12	chr3:120136800-120147600	Enhancers	Adipose Nuclei	Adipose
13	chr3:120136800-120148400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr3:120136800-120148600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:120137000-120149600	Enhancers	Rectal Smooth Muscle	rectum
16	chr3:120137400-120141400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:120137400-120162200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:120137600-120142000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:120137800-120142600	Genic enhancers	Fetal Muscle Leg	muscle
20	chr3:120137800-120161600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:120138200-120142000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:120138200-120142000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr3:120138200-120142000	Weak transcription	Lung	lung
24	chr3:120138200-120142200	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr3:120138200-120145400	Weak transcription	NHEK	skin
26	chr3:120138200-120146400	Weak transcription	Fetal Intestine Large	intestine
27	chr3:120138200-120154200	Weak transcription	HMEC	breast
28	chr3:120138200-120157200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr3:120138200-120162000	Weak transcription	Primary hematopoietic stem cells	blood
30	chr3:120138200-120167800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr3:120138200-120169200	Weak transcription	Gastric	stomach
32	chr3:120138400-120143000	Weak transcription	Fetal Thymus	thymus
33	chr3:120138400-120148600	Genic enhancers	NHDF-Ad	bronchial
34	chr3:120138400-120155600	Weak transcription	Esophagus	oesophagus
35	chr3:120138600-120147800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr3:120138600-120148600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr3:120138800-120150600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr3:120139000-120142000	Enhancers	Fetal Stomach	stomach
39	chr3:120139000-120142200	Weak transcription	Fetal Muscle Trunk	muscle
40	chr3:120139000-120148000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr3:120139200-120145000	Weak transcription	Liver	Liver
42	chr3:120139400-120143200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr3:120139800-120144000	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr3:120140000-120142000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr3:120140200-120143600	Enhancers	Right Ventricle	heart
46	chr3:120140600-120141600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr3:120140600-120141800	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr3:120140600-120142000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr3:120140600-120142000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr3:120140600-120142000	Weak transcription	Skeletal Muscle Male	skeletal muscle

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