Variant report

Variant	rs35278288
Chromosome Location	chr6:12826700-12826701
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:12820824..12822422-chr6:12824948..12827101,2	K562	blood:
2	chr6:12822190..12823999-chr6:12824891..12827143,2	MCF-7	breast:
3	chr6:12820920..12822422-chr6:12824421..12827101,2	K562	blood:

Extended variants
information (count: 126 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs1011188	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs10434854	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10434855	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10498681	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs12525116	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs12525210	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs12526812	1.00[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs12528247	0.96[EUR][1000 genomes]
rs12528721	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs12530470	0.89[CEU][hapmap]
rs13192344	0.97[ASN][1000 genomes]
rs13192509	0.97[ASN][1000 genomes]
rs1332842	0.80[EUR][1000 genomes]
rs1332851	0.89[CEU][hapmap]
rs1412742	0.97[ASN][1000 genomes]
rs1412743	0.97[ASN][1000 genomes]
rs1537334	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1537335	0.97[ASN][1000 genomes]
rs1537336	0.97[ASN][1000 genomes]
rs1537337	0.97[ASN][1000 genomes]
rs1537338	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1571996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1572001	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs16873301	0.81[CEU][hapmap]
rs16873431	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs16873436	0.97[ASN][1000 genomes]
rs16873447	0.97[ASN][1000 genomes]
rs16873449	0.97[ASN][1000 genomes]
rs17616767	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs17617491	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs17617584	1.00[TSI][hapmap]
rs17678734	1.00[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs17679286	0.91[EUR][1000 genomes]
rs2015761	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2026457	0.85[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2065490	0.97[ASN][1000 genomes]
rs2065491	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2151221	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2184027	0.97[ASN][1000 genomes]
rs2876298	1.00[CEU][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs35657920	0.89[ASN][1000 genomes]
rs3945322	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4142300	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4285318	0.91[EUR][1000 genomes]
rs4293998	0.91[EUR][1000 genomes]
rs4577783	1.00[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs4583985	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs4711817	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs4711842	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4711845	0.97[ASN][1000 genomes]
rs4711848	1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs4711856	0.82[MEX][hapmap];0.80[EUR][1000 genomes]
rs4714913	0.97[ASN][1000 genomes]
rs4714930	0.86[ASN][1000 genomes]
rs4714931	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5017386	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs55764622	0.91[EUR][1000 genomes]
rs55879442	0.96[EUR][1000 genomes]
rs56244510	0.91[EUR][1000 genomes]
rs56259669	0.91[EUR][1000 genomes]
rs56270763	0.91[EUR][1000 genomes]
rs56408440	1.00[ASN][1000 genomes]
rs57387500	1.00[ASN][1000 genomes]
rs58666803	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60954427	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6458493	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6458494	0.97[ASN][1000 genomes]
rs6911996	0.89[CEU][hapmap]
rs6915402	0.93[ASN][1000 genomes]
rs6915585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6917097	0.85[CHB][hapmap];0.93[CHD][hapmap];0.88[ASN][1000 genomes]
rs73722820	0.91[EUR][1000 genomes]
rs73722822	0.91[EUR][1000 genomes]
rs73722823	0.91[EUR][1000 genomes]
rs73722845	0.87[EUR][1000 genomes]
rs73722849	0.91[EUR][1000 genomes]
rs7454135	0.86[ASN][1000 genomes]
rs7768030	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296486	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9296487	0.85[CHB][hapmap];0.96[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs9296488	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9296495	0.96[CHD][hapmap];0.85[ASN][1000 genomes]
rs9349344	0.96[ASN][1000 genomes]
rs9349346	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9349350	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9349352	0.97[ASN][1000 genomes]
rs9357486	0.89[CEU][hapmap]
rs9357503	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9367239	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9367240	0.97[ASN][1000 genomes]
rs9369605	0.97[ASN][1000 genomes]
rs9369607	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9369612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9381427	0.90[ASN][1000 genomes]
rs9381435	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9381436	0.97[ASN][1000 genomes]
rs9381439	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9381451	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9395161	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9395162	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9395172	0.88[ASN][1000 genomes]
rs9395185	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[ASN][1000 genomes]
rs9463091	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs9463093	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs9463105	0.91[EUR][1000 genomes]
rs9463114	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs9463117	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs9463119	1.00[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs9463140	0.91[EUR][1000 genomes]
rs9472484	0.89[EUR][1000 genomes]
rs9472511	0.91[EUR][1000 genomes]
rs9472512	0.91[EUR][1000 genomes]
rs9472513	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs9472514	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs9472519	0.85[EUR][1000 genomes]
rs9472520	0.91[EUR][1000 genomes]
rs9472528	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs9472549	1.00[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs9472566	1.00[CEU][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs9472672	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9472752	0.96[CHD][hapmap];0.85[ASN][1000 genomes]
rs950719	0.80[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]

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	esv3521000	chr6:12561306-13128519	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv3521001	chr6:12561306-13128519	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv830587	chr6:12769661-12939875	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv830588	chr6:12793530-12972493	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs35278288	NEDD9	cis	cerebellum	SCAN
rs35278288	GMPR	cis	parietal	SCAN
rs35278288	PHACTR1	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12824600-12827000	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr6:12825800-12826800	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr6:12825800-12826800	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr6:12825800-12826800	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr6:12826000-12830400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr6:12826600-12827600	Enhancers	iPS-18 Cell Line	embryonic stem cell

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