Variant report

Variant	rs12872801
Chromosome Location	chr13:40354200-40354201
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:40352027..40354218-chr13:40364182..40366415,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11618582	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12875311	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12876235	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28635831	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34394770	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4514547	0.82[GIH][hapmap]
rs4569133	0.82[GIH][hapmap]
rs7319041	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7320598	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7986796	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7991151	0.82[GIH][hapmap]
rs7993214	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8002731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9532430	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9532433	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9532434	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9548932	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9594366	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9603603	0.96[CEU][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs9603605	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9603608	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9603612	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9603616	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9943	0.92[CEU][hapmap];0.81[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][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	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1054797	chr13:40198744-40618428	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
3	nsv541755	chr13:40198744-40618428	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
4	nsv832586	chr13:40222880-40379063	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1040458	chr13:40249387-40638129	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12872801	COG6	cis	multi-tissue	Pritchard
rs12872801	LOC646982	cis	parietal	SCAN
rs12872801	COG6	cis	Muscle Skeletal	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40340400-40361200	Weak transcription	Pancreas	Pancrea
2	chr13:40341800-40356600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr13:40342600-40360200	Weak transcription	Fetal Muscle Leg	muscle
4	chr13:40345400-40354800	Weak transcription	Brain Anterior Caudate	brain
5	chr13:40347800-40355200	Enhancers	HUVEC	blood vessel
6	chr13:40350200-40354400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr13:40350200-40357200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr13:40351000-40354400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr13:40351200-40354200	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr13:40351600-40354600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr13:40351800-40354400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr13:40351800-40354400	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr13:40351800-40354600	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr13:40351800-40358400	Weak transcription	Ovary	ovary
15	chr13:40351800-40360200	Weak transcription	Left Ventricle	heart
16	chr13:40352000-40354400	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr13:40352000-40354600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr13:40352000-40361400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr13:40352200-40354400	Enhancers	Primary T cells from cord blood	blood
20	chr13:40352400-40354400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr13:40352400-40354400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr13:40353200-40354600	Enhancers	Osteobl	bone
23	chr13:40353400-40354400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr13:40353400-40354400	Enhancers	Muscle Satellite Cultured Cells	--
25	chr13:40353400-40354400	Enhancers	HSMM	muscle
26	chr13:40353400-40354400	Enhancers	HSMMtube	muscle
27	chr13:40353400-40354600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr13:40353400-40354600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr13:40353400-40357000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr13:40353600-40354200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr13:40353600-40354400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr13:40353600-40355200	Enhancers	NH-A	brain
33	chr13:40353800-40355400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr13:40353800-40358000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr13:40353800-40358400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr13:40353800-40360000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr13:40354000-40358200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr13:40354000-40358800	Weak transcription	NHLF	lung
39	chr13:40354000-40363200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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