Variant report

Variant	rs10841809
Chromosome Location	chr12:21583961-21583962
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:21581278..21584655-chr12:21586014..21590785,5	K562	blood:

Variant related genes	Relation type
ENSG00000121350	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10161011	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10161132	0.83[CHB][hapmap]
rs10437776	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10770808	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10770810	0.87[CHB][hapmap]
rs10770812	0.83[ASN][1000 genomes]
rs10841808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10841810	0.96[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10841815	0.92[CHB][hapmap];0.83[ASN][1000 genomes]
rs10841816	0.82[ASN][1000 genomes]
rs11046050	0.87[CHB][hapmap]
rs11046055	0.92[CHB][hapmap];0.83[ASN][1000 genomes]
rs11046056	0.81[ASN][1000 genomes]
rs11046064	0.92[CHB][hapmap];0.82[ASN][1000 genomes]
rs11046065	0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs11046069	0.83[ASN][1000 genomes]
rs11608659	0.83[ASN][1000 genomes]
rs11608682	0.87[CHB][hapmap]
rs11610942	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs12228018	0.82[ASN][1000 genomes]
rs12372774	0.92[CHB][hapmap];0.81[ASN][1000 genomes]
rs13035	0.87[CHB][hapmap]
rs1476904	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs1476905	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs1476906	0.83[ASN][1000 genomes]
rs1476907	0.92[CHB][hapmap];0.83[ASN][1000 genomes]
rs1860949	0.87[CHB][hapmap]
rs1963817	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs2058463	0.91[CHB][hapmap];0.84[ASN][1000 genomes]
rs2058464	0.92[CHB][hapmap];0.83[ASN][1000 genomes]
rs2110165	0.91[CHB][hapmap];0.84[ASN][1000 genomes]
rs2159948	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs2192183	0.87[CHB][hapmap]
rs2215734	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs2302500	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs2417979	0.87[CHB][hapmap]
rs2417980	0.87[CHB][hapmap]
rs2417981	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs2417982	0.87[CHB][hapmap]
rs2417984	0.92[CHB][hapmap]
rs3752648	0.82[CHB][hapmap]
rs3759229	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs3782660	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs3825287	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs4762828	0.81[ASN][1000 genomes]
rs4762829	0.92[CHB][hapmap];0.83[ASN][1000 genomes]
rs4762830	0.92[CHB][hapmap];0.82[ASN][1000 genomes]
rs4762831	0.92[CHB][hapmap];0.82[ASN][1000 genomes]
rs4762832	0.83[ASN][1000 genomes]
rs4762833	0.83[ASN][1000 genomes]
rs6487222	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs6487223	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs6487228	0.83[ASN][1000 genomes]
rs6487229	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs6487230	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs7134243	0.92[CHB][hapmap];0.83[ASN][1000 genomes]
rs7135390	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs7136175	0.87[CHB][hapmap]
rs7136257	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs7136265	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs7137034	0.87[CHB][hapmap]
rs714356	0.87[CHB][hapmap]
rs714357	0.87[CHB][hapmap]
rs7295570	0.87[CHB][hapmap]
rs7298300	0.83[ASN][1000 genomes]
rs7303408	0.92[CHB][hapmap];0.83[ASN][1000 genomes]
rs7310953	0.92[CHB][hapmap];0.83[ASN][1000 genomes]
rs7314170	0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs738028	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs738029	0.83[ASN][1000 genomes]
rs7957200	0.83[ASN][1000 genomes]
rs7964140	0.82[ASN][1000 genomes]
rs7966443	0.81[ASN][1000 genomes]
rs7970416	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs7980058	0.81[ASN][1000 genomes]
rs7980474	0.83[ASN][1000 genomes]
rs917855	0.83[CHB][hapmap]
rs9788091	0.83[JPT][hapmap]
rs997820	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519603	chr12:21526472-21584709	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv526789	chr12:21555691-21590788	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
3	nsv898895	chr12:21561645-21621891	Weak transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
4	nsv898896	chr12:21561645-21695584	Strong transcription Bivalent Enhancer Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1043936	chr12:21562673-21979030	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	nsv557741	chr12:21578559-22169854	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
7	nsv469163	chr12:21579080-21592357	Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
8	nsv557742	chr12:21579080-21592357	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10841809	LOC642732	Cis_1M	lymphoblastoid	RTeQTL
rs10841809	LOC642732///PYROXD1	Cis_1M	lymphoblastoid	RTeQTL
rs10841809	PYROXD1	Cis_1M	lymphoblastoid	RTeQTL
rs10841809	RECQL	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21581800-21590000	Weak transcription	HUVEC	blood vessel

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