Variant report

Variant	rs1325739
Chromosome Location	chr1:62760110-62760111
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:62695851..62696415-chr1:62759671..62760258,2	MCF-7	breast:
2	chr1:62759537..62760142-chr1:62872912..62873611,2	MCF-7	breast:
3	chr1:62759279..62761889-chr1:62763662..62766108,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000201153	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11799578	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11805988	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11809181	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11809839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1925826	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58577621	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59349044	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61553333	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1009398	chr1:62656660-62780644	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1013582	chr1:62723703-62910632	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases
5	nsv431712	chr1:62759369-62766001	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62753200-62761600	Weak transcription	Pancreas	Pancrea
2	chr1:62753200-62761600	Weak transcription	Right Atrium	heart
3	chr1:62754200-62760200	Weak transcription	Placenta	Placenta
4	chr1:62754400-62773400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:62754800-62765200	Weak transcription	Fetal Heart	heart
6	chr1:62755600-62761000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr1:62756200-62765000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:62756400-62764800	Weak transcription	HepG2	liver
9	chr1:62759600-62760200	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr1:62759800-62760200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:62759800-62760200	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr1:62759800-62760400	Enhancers	HMEC	breast
13	chr1:62759800-62760600	Enhancers	H9 Cell Line	embryonic stem cell
14	chr1:62759800-62760600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:62759800-62761800	Enhancers	Fetal Muscle Trunk	muscle
16	chr1:62759800-62765400	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr1:62759800-62770800	Enhancers	Fetal Muscle Leg	muscle
18	chr1:62760000-62760200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:62760000-62760200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:62760000-62760200	Enhancers	Brain Hippocampus Middle	brain
21	chr1:62760000-62760200	Strong transcription	Fetal Stomach	stomach
22	chr1:62760000-62760400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr1:62760000-62760600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:62760000-62760600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr1:62760000-62760600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:62760000-62760800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr1:62760000-62760800	Bivalent Enhancer	Brain Cingulate Gyrus	brain
28	chr1:62760000-62761200	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr1:62760000-62761200	Weak transcription	HSMMtube	muscle
30	chr1:62760000-62761600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:62760000-62762400	Enhancers	H1 Cell Line	embryonic stem cell

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