Variant report

Variant	rs62446549
Chromosome Location	chr7:26664837-26664838
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:26663687..26665675-chr7:26667700..26669217,2	K562	blood:
2	chr7:26664430..26667382-chr7:26681275..26683540,2	K562	blood:
3	chr7:26663354..26664941-chr7:27195455..27198222,2	K562	blood:

Variant related genes	Relation type
ENSG00000270182	Chromatin interaction
ENSG00000122592	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10230708	0.97[EUR][1000 genomes]
rs10251530	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10252153	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10276138	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1029436	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10452789	0.85[ASN][1000 genomes]
rs10486470	0.83[EUR][1000 genomes]
rs10486471	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11972163	0.83[EUR][1000 genomes]
rs17154152	0.84[EUR][1000 genomes]
rs28639403	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35970226	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4722627	0.82[EUR][1000 genomes]
rs57000259	0.82[EUR][1000 genomes]
rs57999903	0.84[EUR][1000 genomes]
rs58317468	0.82[EUR][1000 genomes]
rs59304553	0.82[EUR][1000 genomes]
rs59446421	0.88[ASN][1000 genomes]
rs59472926	0.88[ASN][1000 genomes]
rs59641892	0.82[EUR][1000 genomes]
rs60101479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60481941	0.88[ASN][1000 genomes]
rs62446548	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62446555	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62447660	0.85[ASN][1000 genomes]
rs62447699	0.83[ASN][1000 genomes]
rs6461960	0.83[EUR][1000 genomes]
rs6943736	0.83[EUR][1000 genomes]
rs6944239	0.83[EUR][1000 genomes]
rs6944318	0.83[EUR][1000 genomes]
rs6960206	0.83[EUR][1000 genomes]
rs6962850	0.99[EUR][1000 genomes]
rs6967136	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6967151	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6967592	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7784174	0.97[EUR][1000 genomes]
rs7801042	0.97[EUR][1000 genomes]
rs7804935	0.99[EUR][1000 genomes]
rs7805328	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029596	chr7:26302739-26737913	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv538804	chr7:26302739-26737913	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1025538	chr7:26482342-27376045	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
4	nsv538805	chr7:26482342-27376045	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	nsv830929	chr7:26587888-26749735	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv1021253	chr7:26653375-26669899	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62446549	HOXA2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26656200-26666600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr7:26656800-26667400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr7:26664000-26665800	Weak transcription	Lung	lung
4	chr7:26664400-26665200	Enhancers	Pancreas	Pancrea
5	chr7:26664600-26665000	Enhancers	Fetal Heart	heart
6	chr7:26664800-26665000	Enhancers	Right Atrium	heart

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