Variant report

Variant	rs2703079
Chromosome Location	chr13:50803670-50803671
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	chr13:50796637..50798644-chr13:50801798..50803965,2	MCF-7	breast:
2	chr13:50801740..50804287-chr13:50809039..50811026,2	K562	blood:

Variant related genes	Relation type
ENSG00000176124	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1007852	0.84[JPT][hapmap]
rs1965800	0.84[JPT][hapmap];0.86[YRI][hapmap]
rs2066629	0.83[JPT][hapmap]
rs2066632	0.84[JPT][hapmap]
rs2066654	0.83[JPT][hapmap]
rs2580187	0.83[JPT][hapmap]
rs2580188	0.83[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.81[ASN][1000 genomes]
rs2740516	0.84[JPT][hapmap]
rs2762059	0.81[CHB][hapmap]
rs2765768	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2812197	0.85[AMR][1000 genomes]
rs706606	0.83[CHB][hapmap]

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	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
2	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
4	esv2752608	chr13:50550099-51054499	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1249 gene(s)	inside rSNPs	diseases
5	nsv832608	chr13:50678628-50888413	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv900076	chr13:50710579-50912578	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv561631	chr13:50761619-50846748	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv974246	chr13:50798236-50805245	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2703079	ALG11	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50796200-50804000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr13:50797000-50804200	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr13:50799000-50803800	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr13:50799400-50804000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr13:50799400-50804000	Weak transcription	NH-A	brain
6	chr13:50799600-50804000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr13:50799600-50804000	Weak transcription	HMEC	breast
8	chr13:50799800-50804000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr13:50799800-50804000	Weak transcription	Osteobl	bone
10	chr13:50800400-50814400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr13:50800800-50804200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr13:50801400-50804000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr13:50801800-50804000	Weak transcription	Primary B cells from peripheral blood	blood
14	chr13:50801800-50804200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr13:50801800-50804600	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr13:50802200-50803800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr13:50802600-50804000	Weak transcription	HSMMtube	muscle
18	chr13:50802600-50804600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr13:50802800-50805800	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr13:50802800-50809200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr13:50803000-50804000	Weak transcription	Dnd41	blood
22	chr13:50803000-50806400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr13:50803000-50807800	Weak transcription	Fetal Thymus	thymus
24	chr13:50803400-50803800	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr13:50803400-50804400	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr13:50803400-50805200	Enhancers	HepG2	liver

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