Variant report

Variant	rs12876235
Chromosome Location	chr13:40351094-40351095
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	chr13:40350876..40353001-chr13:41230658..41232496,2	MCF-7	breast:
2	chr13:40349745..40352056-chr13:40357324..40359153,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11618582	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12872801	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12875311	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28635831	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34394770	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7319041	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7320598	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7986796	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7993214	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8002731	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9532430	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9532433	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9532434	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9548932	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9594366	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9603603	0.88[EUR][1000 genomes]
rs9603605	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9603608	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9603612	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9603616	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9943	0.96[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12876235	COG6	cis	Muscle Skeletal	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40312200-40351200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr13:40327400-40352200	Weak transcription	Primary T cells from cord blood	blood
3	chr13:40340400-40353600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr13:40340400-40361200	Weak transcription	Pancreas	Pancrea
5	chr13:40340600-40351200	Weak transcription	Gastric	stomach
6	chr13:40340600-40351200	Weak transcription	Right Ventricle	heart
7	chr13:40341800-40356600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr13:40342600-40351200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr13:40342600-40360200	Weak transcription	Fetal Muscle Leg	muscle
10	chr13:40342800-40351200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr13:40345400-40354800	Weak transcription	Brain Anterior Caudate	brain
12	chr13:40347800-40355200	Enhancers	HUVEC	blood vessel
13	chr13:40348200-40351600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr13:40348400-40351200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr13:40348400-40351200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr13:40348600-40351800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr13:40349600-40351200	Enhancers	Osteobl	bone
18	chr13:40349600-40351400	Enhancers	HSMM	muscle
19	chr13:40349800-40351200	Weak transcription	Ovary	ovary
20	chr13:40350200-40351200	Enhancers	HSMMtube	muscle
21	chr13:40350200-40351600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr13:40350200-40352200	Enhancers	NHLF	lung
23	chr13:40350200-40354400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr13:40350200-40357200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr13:40350400-40351600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr13:40350600-40351200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr13:40350600-40351800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr13:40350600-40352200	Enhancers	NHDF-Ad	bronchial
29	chr13:40350800-40351200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr13:40350800-40351400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr13:40350800-40351800	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr13:40350800-40352200	Enhancers	NHEK	skin
33	chr13:40350800-40354000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr13:40351000-40351400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
35	chr13:40351000-40351400	Flanking Active TSS	NH-A	brain
36	chr13:40351000-40351800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr13:40351000-40352000	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr13:40351000-40352000	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr13:40351000-40352400	Enhancers	HMEC	breast
40	chr13:40351000-40354400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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