Variant report

Variant	rs6650473
Chromosome Location	chr13:40336903-40336904
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	chr13:40334982..40337230-chr13:40339387..40341631,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12584772	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3012147	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3012153	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3012154	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4603426	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56322803	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6563745	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6563751	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7329513	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9532423	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9532427	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9532435	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9548899	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9548902	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9548903	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9548904	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9548921	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9548923	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9548925	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv471130	chr13:40261945-40350912	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6650473	COG6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40255800-40340200	Weak transcription	Psoas Muscle	Psoas
2	chr13:40267600-40341200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr13:40293000-40340800	Weak transcription	Colon Smooth Muscle	Colon
4	chr13:40294200-40339200	Weak transcription	Fetal Brain Male	brain
5	chr13:40297600-40339800	Weak transcription	Brain Hippocampus Middle	brain
6	chr13:40304600-40340000	Weak transcription	Osteobl	bone
7	chr13:40311400-40347200	Weak transcription	HSMM	muscle
8	chr13:40311600-40339800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr13:40311600-40340000	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr13:40311800-40339800	Weak transcription	Brain Anterior Caudate	brain
11	chr13:40311800-40340000	Weak transcription	Ovary	ovary
12	chr13:40312000-40340000	Weak transcription	Brain Angular Gyrus	brain
13	chr13:40312200-40340000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr13:40312200-40340000	Weak transcription	Pancreas	Pancrea
15	chr13:40312200-40340200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr13:40312200-40351200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr13:40315000-40340200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr13:40325800-40339800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr13:40326200-40339400	Weak transcription	Adipose Nuclei	Adipose
20	chr13:40327400-40344400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr13:40327400-40352200	Weak transcription	Primary T cells from cord blood	blood
22	chr13:40327800-40339400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr13:40327800-40347400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr13:40330000-40345200	Weak transcription	Aorta	Aorta
25	chr13:40330200-40340000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr13:40330400-40339800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr13:40332200-40339200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr13:40332400-40340200	Weak transcription	Esophagus	oesophagus
29	chr13:40335400-40339800	Weak transcription	Liver	Liver

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