Variant report

Variant	rs4603426
Chromosome Location	chr13:40339678-40339679
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:40334982..40337230-chr13:40339387..40341631,2	MCF-7	breast:
2	chr13:40339648..40340487-chr13:40516980..40517545,3	MCF-7	breast:
3	chr13:40338587..40340138-chr13:40344634..40347298,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs12584772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3012147	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3012153	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3012154	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4303351	0.90[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs4329796	0.80[AMR][1000 genomes]
rs4346098	0.82[AMR][1000 genomes]
rs56322803	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6563745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6563751	0.84[EUR][1000 genomes]
rs6650473	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7329513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7988187	0.80[AMR][1000 genomes]
rs7989518	0.80[AMR][1000 genomes]
rs7994943	0.83[JPT][hapmap]
rs9315726	0.80[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes]
rs9532423	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9532427	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9532435	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9548882	0.88[GIH][hapmap];0.81[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes]
rs9548886	0.81[CHD][hapmap];0.88[GIH][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes]
rs9548887	0.84[TSI][hapmap]
rs9548889	0.80[AMR][1000 genomes]
rs9548892	0.82[AMR][1000 genomes]
rs9548899	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9548902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548904	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548921	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548923	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9548925	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9566468	0.80[AMR][1000 genomes]
rs9576878	0.88[GIH][hapmap];0.87[TSI][hapmap]
rs9576883	0.80[AMR][1000 genomes]
rs9576885	0.80[AMR][1000 genomes]
rs9576886	0.80[AMR][1000 genomes]
rs9576888	0.82[AMR][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
rs4603426	COG6	cis	multi-tissue	Pritchard

Chromatin state (count:32 , 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	chr13:40297600-40339800	Weak transcription	Brain Hippocampus Middle	brain
5	chr13:40304600-40340000	Weak transcription	Osteobl	bone
6	chr13:40311400-40347200	Weak transcription	HSMM	muscle
7	chr13:40311600-40339800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr13:40311600-40340000	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr13:40311800-40339800	Weak transcription	Brain Anterior Caudate	brain
10	chr13:40311800-40340000	Weak transcription	Ovary	ovary
11	chr13:40312000-40340000	Weak transcription	Brain Angular Gyrus	brain
12	chr13:40312200-40340000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr13:40312200-40340000	Weak transcription	Pancreas	Pancrea
14	chr13:40312200-40340200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr13:40312200-40351200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr13:40315000-40340200	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr13:40325800-40339800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr13:40327400-40344400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr13:40327400-40352200	Weak transcription	Primary T cells from cord blood	blood
20	chr13:40327800-40347400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr13:40330000-40345200	Weak transcription	Aorta	Aorta
22	chr13:40330200-40340000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr13:40330400-40339800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr13:40332400-40340200	Weak transcription	Esophagus	oesophagus
25	chr13:40335400-40339800	Weak transcription	Liver	Liver
26	chr13:40339200-40342600	Enhancers	Fetal Brain Male	brain
27	chr13:40339200-40342800	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr13:40339400-40342600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr13:40339400-40342600	Enhancers	Adipose Nuclei	Adipose
30	chr13:40339400-40342800	Enhancers	Fetal Brain Female	brain
31	chr13:40339600-40340400	Enhancers	Duodenum Mucosa	Duodenum
32	chr13:40339600-40343200	Enhancers	Brain Germinal Matrix	brain

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