Variant report

Variant	rs11954077
Chromosome Location	chr5:1639658-1639659
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:1634031..1636577-chr5:1639531..1641911,4	MCF-7	breast:
2	chr5:1632420..1636449-chr5:1636560..1641821,6	MCF-7	breast:
3	chr5:1475367..1477969-chr5:1638035..1640520,2	MCF-7	breast:
4	chr5:1632750..1636103-chr5:1636749..1640092,3	K562	blood:
5	chr5:1637235..1639210-chr5:1639365..1642347,2	K562	blood:

Variant related genes	Relation type
ENSG00000188002	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11133831	1.00[ASN][1000 genomes]
rs11948870	1.00[ASN][1000 genomes]
rs11951409	1.00[ASN][1000 genomes]
rs11951807	1.00[ASN][1000 genomes]
rs11951980	1.00[ASN][1000 genomes]
rs11952238	1.00[ASN][1000 genomes]
rs11953233	1.00[ASN][1000 genomes]
rs11955967	1.00[ASN][1000 genomes]
rs11957991	1.00[ASN][1000 genomes]
rs11958097	1.00[ASN][1000 genomes]
rs2883372	1.00[ASN][1000 genomes]
rs4415117	1.00[ASN][1000 genomes]
rs55864560	1.00[ASN][1000 genomes]
rs55867519	1.00[ASN][1000 genomes]
rs55957581	1.00[ASN][1000 genomes]
rs56185279	1.00[ASN][1000 genomes]
rs57587846	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs58452381	1.00[ASN][1000 genomes]
rs58687576	1.00[ASN][1000 genomes]
rs59610035	1.00[ASN][1000 genomes]
rs59656356	1.00[ASN][1000 genomes]
rs59806631	1.00[ASN][1000 genomes]
rs61340395	1.00[ASN][1000 genomes]
rs6867199	1.00[ASN][1000 genomes]
rs6869310	1.00[ASN][1000 genomes]
rs6870117	1.00[ASN][1000 genomes]
rs6871261	1.00[ASN][1000 genomes]
rs6872202	1.00[ASN][1000 genomes]
rs6884318	1.00[ASN][1000 genomes]
rs6888170	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6888910	1.00[ASN][1000 genomes]
rs6889629	1.00[ASN][1000 genomes]
rs6889684	1.00[ASN][1000 genomes]
rs6891099	1.00[ASN][1000 genomes]
rs6898538	1.00[ASN][1000 genomes]
rs72717589	1.00[ASN][1000 genomes]
rs72717593	1.00[ASN][1000 genomes]
rs72717595	1.00[ASN][1000 genomes]
rs72717596	1.00[ASN][1000 genomes]
rs72717598	1.00[ASN][1000 genomes]
rs72717600	1.00[ASN][1000 genomes]
rs72719233	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs73732121	1.00[ASN][1000 genomes]
rs73732122	1.00[ASN][1000 genomes]
rs73732124	1.00[ASN][1000 genomes]
rs73732134	1.00[ASN][1000 genomes]
rs7708447	1.00[ASN][1000 genomes]
rs7716004	1.00[ASN][1000 genomes]
rs7725592	1.00[ASN][1000 genomes]
rs7728463	1.00[ASN][1000 genomes]
rs7728632	1.00[ASN][1000 genomes]
rs7729323	1.00[ASN][1000 genomes]
rs7732756	1.00[ASN][1000 genomes]
rs7736524	1.00[ASN][1000 genomes]
rs7736669	1.00[ASN][1000 genomes]
rs7737033	1.00[ASN][1000 genomes]
rs7737331	1.00[ASN][1000 genomes]

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	nsv933805	chr5:1450724-1941619	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv880740	chr5:1468287-1671200	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	49 gene(s)	inside rSNPs	diseases
3	nsv881554	chr5:1468287-1696932	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	49 gene(s)	inside rSNPs	diseases
4	nsv817407	chr5:1495354-2191460	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
5	nsv881096	chr5:1503610-1671200	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
6	nsv880390	chr5:1612612-1653418	Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv880788	chr5:1629407-1671200	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv881328	chr5:1637461-1671200	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11954077	LOC728613	Cis_1M	lymphoblastoid	RTeQTL
rs11954077	SDHAP3	cis	Whole Blood	GTEx
rs11954077	LOC728613///PDCD6	Cis_1M	lymphoblastoid	RTeQTL
rs11954077	SDHAP3	cis	Esophagus Mucosa	GTEx
rs11954077	SDHAP3	cis	Thyroid	GTEx
rs11954077	RP11-43F13.1	cis	Whole Blood	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1634600-1645000	Weak transcription	Right Atrium	heart
2	chr5:1634600-1645200	Weak transcription	Gastric	stomach
3	chr5:1635200-1640000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr5:1639200-1640400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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