Variant report

Variant	rs9545193
Chromosome Location	chr13:80355961-80355962
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1158596	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1160131	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1414109	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4319636	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7321213	0.92[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7324675	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9318656	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9318657	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9530960	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9545192	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9545204	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9574473	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9574484	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9601268	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv900588	chr13:80216846-80421340	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv900590	chr13:80342186-80421340	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9545193	COMMD6	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:80349600-80357600	Enhancers	Fetal Intestine Large	intestine
2	chr13:80349800-80358600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr13:80350800-80356000	Weak transcription	Fetal Lung	lung
4	chr13:80351000-80356000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr13:80351000-80356000	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr13:80351000-80356200	Weak transcription	HUVEC	blood vessel
7	chr13:80351800-80356200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr13:80351800-80356200	Weak transcription	Duodenum Mucosa	Duodenum
9	chr13:80353200-80358800	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr13:80354000-80356200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr13:80354000-80356800	Weak transcription	Stomach Mucosa	stomach
12	chr13:80354000-80357000	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr13:80354200-80356400	Weak transcription	Brain Substantia Nigra	brain
14	chr13:80354200-80356800	Weak transcription	Small Intestine	intestine
15	chr13:80354400-80356200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr13:80354400-80356400	Weak transcription	Fetal Intestine Small	intestine
17	chr13:80354400-80356800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr13:80354600-80356000	Weak transcription	Fetal Kidney	kidney
19	chr13:80354600-80356000	Weak transcription	Hela-S3	cervix
20	chr13:80354600-80356200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr13:80354600-80356200	Weak transcription	A549	lung
22	chr13:80354600-80356400	Weak transcription	Brain Anterior Caudate	brain
23	chr13:80354600-80356400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr13:80354600-80357000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr13:80354800-80356000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr13:80354800-80356000	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr13:80354800-80356200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr13:80354800-80356400	Weak transcription	Left Ventricle	heart
29	chr13:80354800-80356800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr13:80354800-80357000	Weak transcription	Aorta	Aorta
31	chr13:80354800-80357000	Weak transcription	Psoas Muscle	Psoas
32	chr13:80354800-80357000	Weak transcription	NHEK	skin
33	chr13:80355000-80356000	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr13:80355000-80356000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr13:80355000-80356000	Weak transcription	HSMM	muscle
36	chr13:80355000-80356400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr13:80355000-80356400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr13:80355000-80356400	Weak transcription	Fetal Muscle Leg	muscle
39	chr13:80355000-80356400	Weak transcription	Fetal Thymus	thymus
40	chr13:80355000-80356600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr13:80355000-80356800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr13:80355000-80356800	Weak transcription	NHLF	lung
43	chr13:80355000-80357000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr13:80355000-80357000	Enhancers	Osteobl	bone
45	chr13:80355200-80356400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr13:80355400-80356000	Weak transcription	NHDF-Ad	bronchial
47	chr13:80355600-80356400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr13:80355600-80356600	Enhancers	Muscle Satellite Cultured Cells	--
49	chr13:80355800-80356200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr13:80355800-80356200	Enhancers	iPS-20b Cell Line	embryonic stem cell

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