Variant report

Variant	rs28619135
Chromosome Location	chr8:120870605-120870606
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:120843040..120845421-chr8:120869233..120871945,2	MCF-7	breast:
2	chr8:120866641..120870729-chr8:120883446..120889946,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000064313	Chromatin interaction
ENSG00000155792	Chromatin interaction
ENSG00000245330	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10086801	0.84[ASN][1000 genomes]
rs10108101	0.81[ASN][1000 genomes]
rs10955938	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10955939	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11785110	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11991780	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16893240	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16893243	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16893249	0.84[ASN][1000 genomes]
rs16893252	0.84[ASN][1000 genomes]
rs28700049	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55741337	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55776270	0.84[ASN][1000 genomes]
rs55889147	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58900911	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62526621	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62526622	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62526623	0.84[ASN][1000 genomes]
rs62526624	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62526625	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62526635	0.84[ASN][1000 genomes]
rs62526636	0.84[ASN][1000 genomes]
rs62526637	0.84[ASN][1000 genomes]
rs62526638	0.84[ASN][1000 genomes]
rs62526639	0.84[ASN][1000 genomes]
rs62526640	0.84[ASN][1000 genomes]
rs62526641	0.84[ASN][1000 genomes]
rs62526642	0.84[ASN][1000 genomes]
rs6981251	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6982092	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6987018	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6987100	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6987160	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6987389	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6989803	0.86[ASN][1000 genomes]
rs6994085	0.86[ASN][1000 genomes]
rs7002440	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7007123	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7007265	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72690123	0.84[ASN][1000 genomes]
rs72690128	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72690134	0.84[ASN][1000 genomes]
rs72690137	0.84[ASN][1000 genomes]
rs73705442	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7813113	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7815122	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7815389	0.86[ASN][1000 genomes]
rs7823836	0.84[ASN][1000 genomes]
rs7823910	0.84[ASN][1000 genomes]
rs7823917	0.84[ASN][1000 genomes]
rs7825443	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7828086	0.86[ASN][1000 genomes]
rs7843080	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7843579	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534028	chr8:120348940-120906079	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv949368	chr8:120568034-121019872	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1021071	chr8:120589963-120968317	Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv891418	chr8:120600965-121301474	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv465789	chr8:120636850-120994394	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv612111	chr8:120636850-120994394	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv427826	chr8:120642181-120953395	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs28619135	DSCC1	cis	Adipose Subcutaneous	GTEx
rs28619135	DSCC1	cis	Stomach	GTEx
rs28619135	DSCC1	cis	Skin Sun Exposed Lower leg	GTEx
rs28619135	DSCC1	cis	Thyroid	GTEx
rs28619135	DSCC1	cis	Artery Aorta	GTEx
rs28619135	DSCC1	cis	Heart Left Ventricle	GTEx
rs28619135	DSCC1	cis	Artery Tibial	GTEx
rs28619135	DSCC1	cis	Esophagus Muscularis	GTEx
rs28619135	DSCC1	cis	Nerve Tibial	GTEx
rs28619135	DSCC1	cis	Muscle Skeletal	GTEx
rs28619135	DSCC1	cis	lung	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:120868800-120870800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr8:120868800-120872000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr8:120868800-120872600	Weak transcription	Esophagus	oesophagus
4	chr8:120868800-120879200	Weak transcription	Stomach Mucosa	stomach
5	chr8:120868800-120885600	Weak transcription	Left Ventricle	heart
6	chr8:120869200-120875200	Weak transcription	A549	lung
7	chr8:120869600-120875400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr8:120869600-120885400	Weak transcription	Fetal Lung	lung
9	chr8:120870000-120875200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr8:120870600-120870800	Enhancers	ES-I3 Cell Line	embryonic stem cell

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