Variant report

Variant	rs13145558
Chromosome Location	chr4:122662463-122662464
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:122659671..122662729-chr4:122664166..122666921,4	K562	blood:

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10001092	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10001697	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10001889	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10004284	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10007956	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10012775	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10020581	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10024878	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10028375	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10084948	0.80[AFR][1000 genomes]
rs10212738	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1048433	0.80[AFR][1000 genomes]
rs11098640	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11098641	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11098643	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11724322	0.83[EUR][1000 genomes]
rs11734075	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11934307	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12510839	0.85[AFR][1000 genomes]
rs13104233	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13106764	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs13108419	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs13113338	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13113421	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13114801	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13119055	0.85[AFR][1000 genomes]
rs13128434	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13130789	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs13140070	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs13152701	0.85[AFR][1000 genomes]
rs28394772	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28435300	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs28522256	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs28615388	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28672860	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3217772	0.85[AFR][1000 genomes]
rs34445121	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs35495505	0.85[AFR][1000 genomes]
rs3762840	0.85[AFR][1000 genomes]
rs4075065	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4075066	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4240262	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4240263	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4240264	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4315813	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4361412	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4455438	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4516738	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4833232	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4833234	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4833235	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4833769	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4833770	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4833773	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4833775	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs67150579	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs67775544	0.85[AFR][1000 genomes]
rs6822155	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6827573	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6828650	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7676867	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs769236	0.85[AFR][1000 genomes]
rs7698889	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7699289	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9993206	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9995319	0.85[AFR][1000 genomes]
rs9995322	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9998385	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9998785	0.85[AFR][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	nsv817261	chr4:122085173-123020068	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv997539	chr4:122544104-123274266	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv530157	chr4:122557302-123248756	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv461635	chr4:122633535-122720999	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv595357	chr4:122633535-122720999	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13145558	CCNA2	Cis_1M	lymphoblastoid	RTeQTL
rs13145558	EXOSC9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:122657600-122663200	Enhancers	Fetal Lung	lung
2	chr4:122658000-122662800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr4:122660600-122662600	Weak transcription	Fetal Brain Female	brain
4	chr4:122661400-122663200	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr4:122661400-122664400	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr4:122661400-122665400	Enhancers	Fetal Heart	heart
7	chr4:122661600-122662800	Weak transcription	HSMM	muscle
8	chr4:122661600-122662800	Weak transcription	HSMMtube	muscle
9	chr4:122661800-122663000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
10	chr4:122662000-122662600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:122662000-122663200	Enhancers	Placenta	Placenta
12	chr4:122662000-122664400	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr4:122662000-122664400	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr4:122662200-122662600	Enhancers	Fetal Brain Male	brain
15	chr4:122662200-122662600	Enhancers	Left Ventricle	heart
16	chr4:122662200-122663200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
17	chr4:122662200-122663200	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr4:122662200-122664200	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr4:122662200-122664400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr4:122662400-122662600	Enhancers	Right Atrium	heart
21	chr4:122662400-122663400	Enhancers	Cortex derived primary cultured neurospheres	brain

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