Variant report

Variant	rs13108419
Chromosome Location	chr4:122687238-122687239
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr4:122687176-122687643	H1-hESC	embryonic stem cell:	n/a	n/a
2	MXI1	chr4:122687133-122687297	H1-hESC	embryonic stem cell:	n/a	n/a
3	USF1	chr4:122687204-122687614	H1-hESC	embryonic stem cell:	n/a	chr4:122687475-122687486
4	BHLHE40	chr4:122687209-122687675	K562	blood:	n/a	n/a
5	ZNF263	chr4:122687011-122687850	HEK293-T-REx	kidney:	n/a	n/a
6	MAX	chr4:122687228-122687606	H1-hESC	embryonic stem cell:	n/a	n/a
7	SIN3A	chr4:122687218-122687614	H1-hESC	embryonic stem cell:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC079341.1-5	chr4:122685740-122687963	NR_024365

Variant related genes	Relation type
TMEM155	TF binding region

Extended variants
information (count: 89 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10001092	0.94[EUR][1000 genomes]
rs10001697	0.94[EUR][1000 genomes]
rs10001889	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10004284	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10007956	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10012775	0.94[EUR][1000 genomes]
rs10013916	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10020581	0.94[EUR][1000 genomes]
rs10023020	0.90[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10024878	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs10028375	0.95[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs10084948	0.95[AFR][1000 genomes]
rs10212738	0.94[EUR][1000 genomes]
rs1048433	0.95[AFR][1000 genomes]
rs11098640	0.94[EUR][1000 genomes]
rs11098641	0.93[EUR][1000 genomes]
rs11098643	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11724322	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11734075	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11934307	0.94[EUR][1000 genomes]
rs12510839	1.00[AFR][1000 genomes]
rs13104233	0.94[EUR][1000 genomes]
rs13106764	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13113338	0.80[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs13113421	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs13114801	0.93[EUR][1000 genomes]
rs13117282	0.89[AFR][1000 genomes]
rs13119055	1.00[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs13127488	0.89[AFR][1000 genomes]
rs13128434	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs13130789	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13140070	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13145213	0.80[ASN][1000 genomes]
rs13145558	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs13152701	1.00[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs17005256	0.80[ASN][1000 genomes]
rs28394772	0.94[EUR][1000 genomes]
rs28435300	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28522256	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28615388	0.94[EUR][1000 genomes]
rs28672860	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3217772	1.00[AFR][1000 genomes]
rs34445121	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35341163	0.90[AFR][1000 genomes]
rs35495505	1.00[AFR][1000 genomes]
rs3762840	1.00[AFR][1000 genomes]
rs3811742	0.81[ASN][1000 genomes]
rs4075065	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4075066	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4240262	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs4240263	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4240264	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4315813	0.94[EUR][1000 genomes]
rs4361412	0.90[EUR][1000 genomes]
rs4455438	0.94[EUR][1000 genomes]
rs4516738	0.93[EUR][1000 genomes]
rs4833232	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4833233	0.90[ASN][1000 genomes]
rs4833234	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4833235	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4833236	0.90[AFR][1000 genomes]
rs4833769	0.94[EUR][1000 genomes]
rs4833770	0.94[EUR][1000 genomes]
rs4833773	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4833775	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5004355	0.81[ASN][1000 genomes]
rs67150579	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67775544	1.00[AFR][1000 genomes]
rs6822155	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs6827573	0.94[EUR][1000 genomes]
rs6828650	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6830443	0.81[ASN][1000 genomes]
rs7676867	0.95[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs769236	1.00[AFR][1000 genomes]
rs7698889	0.94[EUR][1000 genomes]
rs7699289	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs951974	0.89[AFR][1000 genomes]
rs966555	0.90[AFR][1000 genomes]
rs9993206	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9995319	1.00[AFR][1000 genomes]
rs9995322	0.94[EUR][1000 genomes]
rs9998385	0.93[EUR][1000 genomes]
rs9998785	1.00[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs9999362	0.81[ASN][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
rs13108419	EXOSC9	Cis_1M	lymphoblastoid	RTeQTL
rs13108419	CCNA2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:122686600-122687400	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
2	chr4:122686600-122687400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
3	chr4:122686600-122687400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
4	chr4:122686600-122687800	Flanking Active TSS	Fetal Heart	heart
5	chr4:122686800-122687400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
6	chr4:122686800-122687400	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr4:122686800-122687600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
8	chr4:122686800-122687600	Active TSS	Right Ventricle	heart
9	chr4:122686800-122689600	Weak transcription	Ovary	ovary
10	chr4:122687000-122687400	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
11	chr4:122687000-122687400	Weak transcription	NHDF-Ad	bronchial
12	chr4:122687000-122687600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr4:122687000-122687800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
14	chr4:122687000-122687800	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
15	chr4:122687200-122687400	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
16	chr4:122687200-122687400	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr4:122687200-122687400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr4:122687200-122687600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
19	chr4:122687200-122687600	Flanking Bivalent TSS/Enh	Placenta	Placenta

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