Variant report

Variant	rs2678829
Chromosome Location	chr8:96028180-96028181
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr8:96028041..96031542-chr8:96035584..96038885,3	K562	blood:
2	chr8:95959016..95961570-chr8:96028062..96029955,2	MCF-7	breast:
3	chr8:95959538..95963295-chr8:96025714..96028383,5	MCF-7	breast:
4	chr8:96022721..96025517-chr8:96026848..96029515,2	MCF-7	breast:
5	chr8:95999262..96000977-chr8:96027577..96029691,2	K562	blood:
6	chr8:96021154..96024035-chr8:96026303..96030842,4	MCF-7	breast:
7	chr8:95961919..95963671-chr8:96025569..96028274,3	MCF-7	breast:
8	chr8:96027034..96028656-chr8:96030290..96032117,2	K562	blood:
9	chr8:96026673..96028534-chr8:96030617..96033209,2	K562	blood:
10	chr8:96025997..96028447-chr8:96030122..96031980,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000164938	Chromatin interaction
ENSG00000253878	Chromatin interaction
ENSG00000156170	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10086541	1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10087402	0.83[GIH][hapmap]
rs10089123	0.83[GIH][hapmap]
rs10092003	0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10093594	1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10096455	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10097930	0.88[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10098197	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10098453	1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10100089	1.00[ASN][1000 genomes]
rs10103841	0.83[ASN][1000 genomes]
rs10105437	0.93[ASN][1000 genomes]
rs10106491	0.93[ASN][1000 genomes]
rs10111154	0.88[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10111300	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10112230	0.93[ASN][1000 genomes]
rs10113545	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1031388	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11774085	1.00[ASN][1000 genomes]
rs11776189	0.88[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11779506	0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11780931	0.88[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11781001	0.93[ASN][1000 genomes]
rs11781040	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11781619	0.84[ASN][1000 genomes]
rs11784178	1.00[ASN][1000 genomes]
rs11786380	1.00[ASN][1000 genomes]
rs11786878	0.93[ASN][1000 genomes]
rs13279040	0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1545480	0.85[CEU][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.85[MKK][hapmap];0.81[TSI][hapmap];0.87[ASN][1000 genomes]
rs16917224	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16917233	0.88[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2340536	0.84[ASN][1000 genomes]
rs2599711	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2599713	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2599714	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2599715	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2678823	0.94[ASW][hapmap];1.00[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28363725	1.00[ASN][1000 genomes]
rs28378156	1.00[ASN][1000 genomes]
rs28406132	1.00[ASN][1000 genomes]
rs28419772	1.00[ASN][1000 genomes]
rs28440026	1.00[ASN][1000 genomes]
rs28477467	0.93[ASN][1000 genomes]
rs28496357	1.00[ASN][1000 genomes]
rs28616734	1.00[ASN][1000 genomes]
rs28651964	1.00[ASN][1000 genomes]
rs28712702	1.00[ASN][1000 genomes]
rs34700722	1.00[ASN][1000 genomes]
rs35518242	0.81[ASN][1000 genomes]
rs4323442	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs56901035	0.93[ASN][1000 genomes]
rs57925408	0.87[ASN][1000 genomes]
rs6471505	1.00[ASN][1000 genomes]
rs6471506	0.97[ASN][1000 genomes]
rs6651271	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6651272	0.88[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6985880	1.00[ASN][1000 genomes]
rs6989862	1.00[ASN][1000 genomes]
rs7002940	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7008542	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs71532343	0.81[ASN][1000 genomes]
rs73276406	1.00[ASN][1000 genomes]
rs73276417	1.00[ASN][1000 genomes]
rs73276437	0.93[ASN][1000 genomes]
rs73276439	0.93[ASN][1000 genomes]
rs73276444	0.93[ASN][1000 genomes]
rs7812312	0.88[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7818688	1.00[ASN][1000 genomes]
rs7826046	0.90[ASN][1000 genomes]
rs7826196	1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7832570	1.00[ASN][1000 genomes]
rs7842703	0.90[ASN][1000 genomes]
rs7842715	0.97[ASN][1000 genomes]
rs9297950	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9297951	0.96[GIH][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017301	chr8:95273503-96248352	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv539680	chr8:95273503-96248352	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS 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 miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv508520	chr8:95939373-96140068	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2678829	MATN2	cis	parietal	SCAN
rs2678829	C8orf38	cis	cerebellum	SCAN
rs2678829	INTS8	Cis_1M	lymphoblastoid	RTeQTL
rs2678829	C8orf38	Cis_1M	lymphoblastoid	RTeQTL
rs2678829	HRSP12	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:96003200-96032600	Weak transcription	Gastric	stomach
2	chr8:96009000-96036400	Weak transcription	Spleen	Spleen
3	chr8:96023200-96030200	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr8:96023400-96029000	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr8:96023400-96032600	Weak transcription	Right Atrium	heart
6	chr8:96023400-96036600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr8:96024800-96036400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr8:96026400-96033600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr8:96026800-96032600	Weak transcription	Left Ventricle	heart
10	chr8:96026800-96036400	Weak transcription	HMEC	breast

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