Variant report

Variant	rs10876099
Chromosome Location	chr12:51231061-51231062
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51156191..51157743-chr12:51230542..51233377,2	MCF-7	breast:
2	chr12:51229364..51231906-chr12:51476163..51477901,2	MCF-7	breast:
3	chr12:51230523..51233092-chr12:51235059..51236989,2	MCF-7	breast:
4	chr12:51230105..51232434-chr12:51237161..51239319,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123268	Chromatin interaction
ENSG00000243075	Chromatin interaction
ENSG00000110925	Chromatin interaction
ENSG00000186452	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10160844	0.89[ASN][1000 genomes]
rs10459237	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10459238	1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs10459239	1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs10747595	0.93[ASN][1000 genomes]
rs10747596	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10747597	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10747599	1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs10783393	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10783394	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10783395	1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs10783404	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs10783405	1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs10783406	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs10876100	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10876105	0.90[ASN][1000 genomes]
rs10876115	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10876119	0.91[ASN][1000 genomes]
rs1096030	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs1096031	0.91[ASN][1000 genomes]
rs1103441	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs11169587	1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs11169588	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11169589	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11169592	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11169602	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169603	0.88[ASN][1000 genomes]
rs11169608	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169609	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169610	0.93[ASN][1000 genomes]
rs11169612	0.93[ASN][1000 genomes]
rs11169614	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs11495280	0.89[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs11533636	0.92[ASN][1000 genomes]
rs12578465	0.92[ASN][1000 genomes]
rs12578466	0.92[ASN][1000 genomes]
rs12581103	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1362964	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1583697	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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1631348	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1642997	0.89[ASN][1000 genomes]
rs1643004	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1659375	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554852	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2554854	0.93[ASN][1000 genomes]
rs3752667	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4483656	0.93[ASN][1000 genomes]
rs4542479	0.81[ASN][1000 genomes]
rs4768926	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4768937	1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs4768938	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs4768939	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7131969	0.81[ASN][1000 genomes]
rs73100855	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7979616	0.93[ASN][1000 genomes]
rs829120	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs829122	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829126	0.87[ASN][1000 genomes]
rs829128	0.87[CHB][hapmap];0.82[CHD][hapmap];0.90[ASN][1000 genomes]
rs829129	0.90[ASN][1000 genomes]
rs829131	1.00[CHB][hapmap];0.86[CHD][hapmap];0.83[JPT][hapmap]
rs829132	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs829139	0.90[ASN][1000 genomes]
rs829141	1.00[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs829142	1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs829143	1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs829144	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs844175	1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs860476	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv899078	chr12:51213433-51286750	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10876099	KRT79	cis	cerebellum	SCAN
rs10876099	TUBA1B	cis	cerebellum	SCAN
rs10876099	LASS5	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51228400-51235200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:51228400-51236600	Weak transcription	Gastric	stomach
3	chr12:51230800-51236000	Weak transcription	Pancreas	Pancrea

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