Variant report

Variant	rs28435300
Chromosome Location	chr4:122709412-122709413
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:122707279..122709702-chr4:122712277..122713983,2	MCF-7	breast:
2	chr4:122707344..122709734-chr4:122714569..122716206,2	MCF-7	breast:
3	chr4:122616437..122619642-chr4:122706327..122710278,3	K562	blood:

Variant related genes	Relation type
ENSG00000164111	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10001092	0.86[EUR][1000 genomes]
rs10001697	0.86[EUR][1000 genomes]
rs10001889	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10004284	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10007956	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10012775	0.86[EUR][1000 genomes]
rs10013916	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10020581	0.86[EUR][1000 genomes]
rs10023020	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10024820	0.96[ASN][1000 genomes]
rs10024878	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10028375	0.95[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs10084948	0.95[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10212738	0.86[EUR][1000 genomes]
rs1048433	0.95[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs11098640	0.86[EUR][1000 genomes]
rs11098641	0.85[EUR][1000 genomes]
rs11098643	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11724322	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11733882	0.96[ASN][1000 genomes]
rs11734075	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11934307	0.86[EUR][1000 genomes]
rs12510839	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs13104233	0.86[EUR][1000 genomes]
rs13106764	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13108419	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];0.82[EUR][1000 genomes]
rs13113421	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs13114801	0.85[EUR][1000 genomes]
rs13117282	0.89[AFR][1000 genomes]
rs13119055	1.00[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs13127488	0.89[AFR][1000 genomes]
rs13128434	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs13130789	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13140070	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13145213	0.97[ASN][1000 genomes]
rs13145558	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs13152701	1.00[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs17005256	0.97[ASN][1000 genomes]
rs2271176	0.92[ASN][1000 genomes]
rs28394772	0.86[EUR][1000 genomes]
rs28522256	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28615388	0.86[EUR][1000 genomes]
rs28672860	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3217772	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs34445121	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35341163	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs35495505	1.00[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs3762840	1.00[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3811742	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4075065	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4075066	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4240262	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4240263	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4240264	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4315813	0.86[EUR][1000 genomes]
rs4361412	0.82[EUR][1000 genomes]
rs4455438	0.86[EUR][1000 genomes]
rs4516738	0.85[EUR][1000 genomes]
rs4833232	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4833233	0.92[ASN][1000 genomes]
rs4833234	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4833235	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4833236	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4833769	0.86[EUR][1000 genomes]
rs4833770	0.86[EUR][1000 genomes]
rs4833773	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4833775	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5004355	0.98[ASN][1000 genomes]
rs67150579	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67775544	1.00[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6811867	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6822155	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6827573	0.86[EUR][1000 genomes]
rs6828650	0.80[AFR][1000 genomes]
rs6830443	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6845901	0.95[ASN][1000 genomes]
rs7676867	0.95[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs769236	1.00[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7698889	0.86[EUR][1000 genomes]
rs7699289	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs951974	0.89[AFR][1000 genomes]
rs966555	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9993206	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs9995319	1.00[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9995322	0.86[EUR][1000 genomes]
rs9998385	0.85[EUR][1000 genomes]
rs9998785	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9999362	0.98[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
rs28435300	CCNA2	Cis_1M	lymphoblastoid	RTeQTL
rs28435300	EXOSC9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:122706800-122710400	Weak transcription	HUVEC	blood vessel
2	chr4:122706800-122713200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr4:122706800-122713200	Enhancers	NHDF-Ad	bronchial
4	chr4:122707000-122710400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:122707000-122711400	Weak transcription	A549	lung
6	chr4:122707200-122709800	Enhancers	Muscle Satellite Cultured Cells	--
7	chr4:122707200-122710600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:122707400-122710400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr4:122707400-122710400	Weak transcription	Hela-S3	cervix
10	chr4:122707400-122710600	Weak transcription	HMEC	breast
11	chr4:122707600-122709600	Weak transcription	NHLF	lung
12	chr4:122707600-122710200	Weak transcription	NHEK	skin
13	chr4:122707600-122711000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr4:122708000-122710600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr4:122708000-122711200	Weak transcription	Fetal Heart	heart
16	chr4:122708800-122713000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr4:122708800-122713600	Enhancers	Osteobl	bone
18	chr4:122709000-122713600	Enhancers	HSMM	muscle
19	chr4:122709200-122709600	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr4:122709200-122709600	Enhancers	GM12878-XiMat	blood
21	chr4:122709200-122709800	Enhancers	K562	blood
22	chr4:122709200-122711000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr4:122709200-122713000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr4:122709400-122709800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr4:122709400-122709800	Enhancers	HSMMtube	muscle
26	chr4:122709400-122711800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr4:122709400-122713600	Enhancers	NH-A	brain

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