Variant report

Variant	rs6592253
Chromosome Location	chr11:85302342-85302343
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:84433336..84434202-chr11:85301668..85302606,6	MCF-7	breast:
2	chr11:84491944..84492445-chr11:85301546..85302502,2	MCF-7	breast:
3	chr11:84269078..84270239-chr11:85301825..85302485,3	MCF-7	breast:
4	chr11:84511565..84512221-chr11:85301607..85302438,2	MCF-7	breast:
5	chr11:84435745..84436679-chr11:85301971..85302607,2	MCF-7	breast:

Extended variants
information (count: 129 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs10501595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11234359	0.95[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs11603984	0.83[ASN][1000 genomes]
rs11604028	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11605203	0.82[ASN][1000 genomes]
rs11606688	0.83[AFR][1000 genomes]
rs11607685	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11820071	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1192	1.00[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.84[MKK][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1214001	1.00[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12417341	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12419172	0.89[ASW][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MKK][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12420907	0.81[ASN][1000 genomes]
rs1354397	0.95[CHB][hapmap];0.84[CHD][hapmap]
rs1425223	0.84[ASN][1000 genomes]
rs1504027	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1504029	0.81[ASN][1000 genomes]
rs158217	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17148254	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17148293	0.93[ASN][1000 genomes]
rs17148306	0.92[ASN][1000 genomes]
rs17208492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17208519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17810659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1806414	0.86[EUR][1000 genomes]
rs184057	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs185932	0.86[EUR][1000 genomes]
rs1863256	0.80[ASN][1000 genomes]
rs188311	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs1892872	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1954757	0.86[EUR][1000 genomes]
rs1991923	0.90[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs207060	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2162055	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2290823	1.00[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2467059	1.00[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs2512800	0.86[EUR][1000 genomes]
rs286494	0.86[EUR][1000 genomes]
rs286499	0.94[CHB][hapmap]
rs286509	0.86[EUR][1000 genomes]
rs286512	0.86[EUR][1000 genomes]
rs286513	0.95[CHB][hapmap]
rs286515	0.95[CHB][hapmap]
rs286521	0.86[EUR][1000 genomes]
rs286522	0.86[EUR][1000 genomes]
rs286523	0.82[EUR][1000 genomes]
rs286524	0.86[EUR][1000 genomes]
rs286525	0.86[EUR][1000 genomes]
rs286530	0.83[EUR][1000 genomes]
rs286531	0.86[EUR][1000 genomes]
rs286534	0.86[EUR][1000 genomes]
rs286537	0.86[EUR][1000 genomes]
rs286538	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs286539	0.86[EUR][1000 genomes]
rs286540	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs286541	0.85[EUR][1000 genomes]
rs290175	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs290177	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs290178	0.85[ASN][1000 genomes]
rs290182	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs290186	1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.82[LWK][hapmap];0.89[ASN][1000 genomes]
rs290194	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs290196	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs290199	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs35097455	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35844123	0.95[ASN][1000 genomes]
rs4280023	0.89[ASN][1000 genomes]
rs4943918	0.94[CHB][hapmap]
rs4943925	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4944520	0.80[ASN][1000 genomes]
rs4944522	0.82[ASN][1000 genomes]
rs4944527	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4944529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4944531	1.00[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.95[ASN][1000 genomes]
rs4944532	0.93[ASN][1000 genomes]
rs497698	0.97[ASN][1000 genomes]
rs510948	0.88[JPT][hapmap]
rs537266	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs537604	0.88[JPT][hapmap]
rs55739259	0.89[ASN][1000 genomes]
rs55933855	0.82[ASN][1000 genomes]
rs56073783	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56238215	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56256400	0.82[ASN][1000 genomes]
rs56273824	0.83[ASN][1000 genomes]
rs56321405	0.83[ASN][1000 genomes]
rs56579	1.00[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs56737296	0.89[ASN][1000 genomes]
rs57223077	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs573766	0.89[CHB][hapmap];0.92[JPT][hapmap]
rs578324	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs58152312	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs583122	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs58931064	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59082411	0.81[ASN][1000 genomes]
rs592712	0.88[JPT][hapmap]
rs60484561	0.83[ASN][1000 genomes]
rs60838923	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs609012	0.88[JPT][hapmap]
rs61133973	0.86[ASN][1000 genomes]
rs61286868	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs613973	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs62388	0.86[EUR][1000 genomes]
rs639688	0.81[JPT][hapmap]
rs650036	0.94[JPT][hapmap]
rs653559	0.94[JPT][hapmap]
rs6592252	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs681044	0.88[JPT][hapmap]
rs688741	0.94[JPT][hapmap]
rs7108132	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7108137	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7110363	0.95[CHB][hapmap]
rs7115250	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7119617	1.00[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.90[ASN][1000 genomes]
rs73499156	0.83[ASN][1000 genomes]
rs73499163	0.83[ASN][1000 genomes]
rs7939217	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7943586	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7948778	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs881121	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs947861	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs947862	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs947863	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[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];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051155	chr11:85006564-85721261	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv541110	chr11:85006564-85721261	Enhancers Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv898047	chr11:85180409-85377707	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	esv2758279	chr11:85180480-85603988	Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	esv2759845	chr11:85180480-85603988	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
6	nsv898048	chr11:85206156-85404138	Flanking Active TSS Genic enhancers Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6592253	CCDC89	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85300400-85303800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:85300400-85310200	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr11:85300600-85304600	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr11:85300800-85304000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr11:85301000-85304200	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr11:85301400-85304200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr11:85302200-85302400	Enhancers	Fetal Stomach	stomach

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