Variant report

Variant	rs2896454
Chromosome Location	chr8:86060072-86060073
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:85538381..85538975-chr8:86059742..86060294,2	MCF-7	breast:
2	chr8:86059423..86060332-chr8:86201778..86202999,3	MCF-7	breast:
3	chr8:86060046..86062582-chr8:86088601..86090458,2	MCF-7	breast:
4	chr8:86059490..86060356-chr8:86202019..86202533,2	K562	blood:
5	chr8:86059254..86060308-chr8:86202052..86203050,5	MCF-7	breast:
6	chr8:86058766..86061369-chr8:86087811..86090336,2	MCF-7	breast:
7	chr8:86059388..86060135-chr8:86132558..86133520,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000133740	Chromatin interaction
ENSG00000254208	Chromatin interaction
ENSG00000185015	Chromatin interaction
ENSG00000176731	Chromatin interaction
ENSG00000260493	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10088120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10090196	0.86[JPT][hapmap];0.85[TSI][hapmap]
rs10091577	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10091710	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10100442	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10104630	0.90[JPT][hapmap]
rs1021583	0.95[JPT][hapmap]
rs11261468	0.80[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap]
rs11261471	0.91[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap]
rs12541445	0.91[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap]
rs12543256	0.95[JPT][hapmap]
rs12544332	0.86[JPT][hapmap]
rs12546106	0.95[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs12549421	0.88[ASN][1000 genomes]
rs12550160	0.95[JPT][hapmap]
rs12926	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1303806	0.82[JPT][hapmap]
rs13249364	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13259399	0.86[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs13269031	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13269739	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1390711	0.82[JPT][hapmap]
rs1496531	0.86[JPT][hapmap]
rs1496532	0.86[JPT][hapmap]
rs1553015	0.82[JPT][hapmap];0.88[MEX][hapmap]
rs16913600	0.82[CEU][hapmap];0.97[GIH][hapmap];0.82[TSI][hapmap]
rs16913681	0.95[JPT][hapmap]
rs16913721	0.86[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs17740658	0.95[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs1908762	0.90[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs1995056	0.87[MEX][hapmap]
rs1995057	0.91[JPT][hapmap]
rs1995058	0.82[JPT][hapmap]
rs2006767	0.86[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs2132589	0.95[JPT][hapmap];0.85[TSI][hapmap]
rs2278459	0.91[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs2279701	0.91[JPT][hapmap]
rs2291786	0.95[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs2291787	0.91[JPT][hapmap]
rs2403082	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2403083	0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2403084	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2403085	0.86[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2403086	0.86[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2403088	1.00[CEU][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2403089	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2403104	0.82[JPT][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap]
rs28621707	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2896452	0.91[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap]
rs34103685	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34527380	0.93[ASN][1000 genomes]
rs3779899	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3779901	0.95[JPT][hapmap]
rs3808538	0.86[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap]
rs3808539	0.82[JPT][hapmap]
rs4150859	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4150862	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4150865	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4150867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4150868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4150869	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4150884	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4150893	0.86[CEU][hapmap];0.82[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4150897	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4150909	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4150942	0.86[CEU][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs4150944	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4150964	0.95[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs4150974	0.95[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs4150977	0.95[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs4609189	0.95[JPT][hapmap]
rs4739700	0.86[JPT][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap]
rs4740043	1.00[CEU][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4740044	0.86[JPT][hapmap]
rs4740045	0.95[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs4740049	0.82[JPT][hapmap];0.88[MEX][hapmap]
rs62527168	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62527173	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6605609	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6605610	0.95[JPT][hapmap]
rs6605611	0.95[JPT][hapmap]
rs6605624	0.90[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs6605625	0.84[EUR][1000 genomes]
rs6986704	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6990449	0.86[JPT][hapmap]
rs6993387	0.86[JPT][hapmap]
rs6994113	0.95[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs7001359	0.91[JPT][hapmap]
rs7004765	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7008032	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7008772	0.86[JPT][hapmap]
rs7010228	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7011926	0.82[JPT][hapmap];0.88[MEX][hapmap]
rs7015758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72682904	0.81[ASN][1000 genomes]
rs7814435	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7818090	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7818163	0.86[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs7823218	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7826589	0.85[JPT][hapmap]
rs7827175	0.95[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs7829050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7829144	0.80[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap]
rs7841142	0.80[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap]
rs7842013	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs903895	0.82[JPT][hapmap]
rs903896	0.82[JPT][hapmap];0.88[MEX][hapmap]
rs903897	0.82[JPT][hapmap]
rs9692962	0.90[JPT][hapmap]

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	esv3481417	chr8:85279453-86145229	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv3481418	chr8:85279453-86145229	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv1797206	chr8:86023237-86060072	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	esv1800945	chr8:86030101-86060072	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2896454	C8orf59	Cis_1M	lymphoblastoid	RTeQTL
rs2896454	LRRCC1	cis	Artery Tibial	GTEx
rs2896454	C8orf59	cis	parietal	SCAN
rs2896454	LRRCC1	Cis_1M	lymphoblastoid	RTeQTL
rs2896454	LRRCC1	cis	parietal	SCAN
rs2896454	CA13	cis	cerebellum	SCAN
rs2896454	LRRCC1	cis	Esophagus Mucosa	GTEx
rs2896454	C8orf59	cis	cerebellum	SCAN
rs2896454	LRRCC1	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:86020400-86062600	Weak transcription	Pancreas	Pancrea
2	chr8:86037000-86061200	Weak transcription	Brain Anterior Caudate	brain
3	chr8:86040600-86062000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr8:86046600-86064800	Weak transcription	Thymus	Thymus
5	chr8:86046600-86065800	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr8:86049400-86065800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr8:86050800-86061400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr8:86055000-86062400	Weak transcription	Dnd41	blood
9	chr8:86058800-86060200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr8:86059000-86060400	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr8:86059400-86060400	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr8:86059400-86060600	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr8:86059600-86060400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr8:86059800-86060200	Enhancers	Fetal Thymus	thymus
15	chr8:86059800-86060400	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr8:86059800-86060400	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr8:86060000-86060200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr8:86060000-86060200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr8:86060000-86060400	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr8:86060000-86062400	Weak transcription	K562	blood

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