Variant report

Variant	rs9548889
Chromosome Location	chr13:40277477-40277478
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:40276171..40277739-chr8:64083128..64085038,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12584772	0.81[AMR][1000 genomes]
rs4329796	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4346098	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4570710	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4603426	0.80[AMR][1000 genomes]
rs7988187	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7989518	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7994943	0.94[ASN][1000 genomes]
rs9315726	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9532423	0.82[AMR][1000 genomes]
rs9548849	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9548874	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9548882	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9548886	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548887	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9548890	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9548892	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9548902	0.81[AMR][1000 genomes]
rs9548903	0.81[AMR][1000 genomes]
rs9548925	0.80[AMR][1000 genomes]
rs9566464	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9566468	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9576879	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9576883	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9576885	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9576886	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9576888	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9548889	COG6	Cis_1M	lymphoblastoid	RTeQTL
rs9548889	COG6	cis	multi-tissue	Pritchard

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40231000-40286000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr13:40233000-40295600	Weak transcription	Pancreas	Pancrea
3	chr13:40238000-40291600	Weak transcription	Fetal Intestine Small	intestine
4	chr13:40246400-40297400	Weak transcription	HUVEC	blood vessel
5	chr13:40255000-40291200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr13:40255000-40306000	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr13:40255200-40291000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr13:40255600-40283600	Weak transcription	Fetal Brain Male	brain
9	chr13:40255800-40283800	Weak transcription	Brain Anterior Caudate	brain
10	chr13:40255800-40340200	Weak transcription	Psoas Muscle	Psoas
11	chr13:40257600-40310800	Weak transcription	Brain Germinal Matrix	brain
12	chr13:40258200-40289800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr13:40262600-40294000	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr13:40262800-40279200	Weak transcription	HepG2	liver
15	chr13:40262800-40285600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr13:40262800-40286800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr13:40262800-40287200	Weak transcription	Fetal Muscle Leg	muscle
18	chr13:40262800-40291600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr13:40262800-40291600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr13:40262800-40291800	Weak transcription	Left Ventricle	heart
21	chr13:40262800-40293600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr13:40262800-40311000	Weak transcription	Aorta	Aorta
23	chr13:40262800-40311000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr13:40263000-40285600	Weak transcription	Duodenum Mucosa	Duodenum
25	chr13:40263000-40288600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr13:40263000-40297200	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr13:40263200-40288600	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr13:40263200-40290600	Weak transcription	Primary B cells from cord blood	blood
29	chr13:40263200-40302600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr13:40263400-40291000	Weak transcription	Fetal Heart	heart
31	chr13:40263400-40293400	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr13:40263400-40293800	Weak transcription	Dnd41	blood
33	chr13:40263600-40283600	Weak transcription	Primary hematopoietic stem cells	blood
34	chr13:40263600-40286600	Weak transcription	Fetal Brain Female	brain
35	chr13:40263600-40291600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr13:40264000-40278800	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr13:40264600-40285800	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr13:40264600-40289600	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr13:40264600-40293800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr13:40267000-40297400	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr13:40267200-40286000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr13:40267200-40286800	Weak transcription	NHLF	lung
43	chr13:40267200-40290800	Weak transcription	Fetal Lung	lung
44	chr13:40267200-40293400	Weak transcription	NHDF-Ad	bronchial
45	chr13:40267200-40296800	Weak transcription	Brain Hippocampus Middle	brain
46	chr13:40267200-40296800	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr13:40267200-40297000	Weak transcription	Brain Cingulate Gyrus	brain
48	chr13:40267600-40341200	Weak transcription	Rectal Smooth Muscle	rectum
49	chr13:40269200-40293400	Weak transcription	NH-A	brain
50	chr13:40269600-40291600	Weak transcription	Primary monocytes fromperipheralblood	blood

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