Variant report

Variant	rs466962
Chromosome Location	chr5:40803521-40803522
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:40802285..40804990-chr5:40806430..40808418,3	K562	blood:
2	chr5:40802145..40803707-chr5:40812123..40813694,2	K562	blood:
3	chr5:40802266..40804575-chr5:40807090..40808775,2	MCF-7	breast:
4	chr5:40796800..40800335-chr5:40800670..40804865,6	MCF-7	breast:
5	chr5:40802997..40805283-chr5:40828137..40831104,3	MCF-7	breast:
6	chr5:40793843..40796817-chr5:40803354..40805786,3	K562	blood:
7	chr5:40802676..40804762-chr5:40806343..40808441,2	MCF-7	breast:
8	chr5:40752834..40759871-chr5:40793841..40803866,19	K562	blood:
9	chr5:40754690..40758108-chr5:40800193..40803866,6	K562	blood:

No data

Variant related genes	Relation type
ENSG00000113638	Chromatin interaction
ENSG00000132356	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10056345	0.83[ASN][1000 genomes]
rs10060234	0.83[ASN][1000 genomes]
rs1097546	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13355305	0.83[ASN][1000 genomes]
rs154268	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs154275	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs154280	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs154281	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs154284	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs171605	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs171606	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs193864	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2008763	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2161521	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs249413	0.83[ASN][1000 genomes]
rs249414	0.85[ASN][1000 genomes]
rs249416	0.85[ASN][1000 genomes]
rs249420	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs249422	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs249423	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs249425	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs249428	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs249429	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs249437	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs249438	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs257009	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28569300	0.84[ASN][1000 genomes]
rs29740	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs29742	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs29743	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs29744	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4277957	0.83[ASN][1000 genomes]
rs4285273	0.83[ASN][1000 genomes]
rs4315964	0.83[ASN][1000 genomes]
rs4315965	0.83[ASN][1000 genomes]
rs432071	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs434778	0.87[ASN][1000 genomes]
rs4383756	0.83[ASN][1000 genomes]
rs447810	0.87[ASN][1000 genomes]
rs453037	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs461404	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs466108	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4957344	0.83[ASN][1000 genomes]
rs4957351	0.81[EUR][1000 genomes]
rs59069340	0.83[ASN][1000 genomes]
rs59920139	0.83[ASN][1000 genomes]
rs6451535	0.81[ASN][1000 genomes]
rs6451537	0.83[ASN][1000 genomes]
rs6871999	0.83[ASN][1000 genomes]
rs6896993	0.83[ASN][1000 genomes]
rs6897470	0.83[EUR][1000 genomes]
rs7708680	0.83[ASN][1000 genomes]
rs7711806	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7726237	0.81[ASN][1000 genomes]
rs7737044	0.83[ASN][1000 genomes]
rs837101	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881377	chr5:40753877-40810426	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv881070	chr5:40753877-40827307	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv880438	chr5:40753877-40900717	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	160 gene(s)	inside rSNPs	diseases
4	nsv597877	chr5:40796746-40848803	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	158 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs466962	TTC33	Cis_1M	lymphoblastoid	RTeQTL
rs466962	RPL37	Cis_1M	lymphoblastoid	RTeQTL
rs466962	PRKAA1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40799800-40803800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr5:40800200-40808200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr5:40800200-40808400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr5:40800600-40808200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr5:40802000-40803600	Flanking Active TSS	K562	blood
6	chr5:40802000-40803800	Enhancers	HepG2	liver

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