Variant report

Variant	rs4257872
Chromosome Location	chr6:133376141-133376142
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:133371252..133373949-chr6:133374893..133377251,2	K562	blood:

Extended variants
information (count: 67 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10457001	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10457002	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10457599	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10457602	0.85[CEU][hapmap]
rs10457603	0.85[CEU][hapmap]
rs12192002	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12192605	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12193118	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12194836	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12197849	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12198619	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12199972	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12201315	0.85[CEU][hapmap]
rs12205139	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12210093	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12212715	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12213877	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1418702	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17062051	0.82[CHB][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs2011426	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4077767	0.86[EUR][1000 genomes]
rs4077768	0.82[EUR][1000 genomes]
rs4273707	0.80[EUR][1000 genomes]
rs4273708	0.80[EUR][1000 genomes]
rs4895949	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4895952	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57161827	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58835706	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62428455	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62430561	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62430580	0.82[EUR][1000 genomes]
rs62430581	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62430582	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62430588	0.80[EUR][1000 genomes]
rs62430590	0.80[EUR][1000 genomes]
rs6569863	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6902347	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6908361	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6911954	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6915521	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6927627	0.80[EUR][1000 genomes]
rs6933214	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6935070	0.80[EUR][1000 genomes]
rs6935480	0.80[EUR][1000 genomes]
rs6935677	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6936410	0.80[EUR][1000 genomes]
rs6940959	0.80[EUR][1000 genomes]
rs72557636	0.86[ASN][1000 genomes]
rs7738156	0.80[EUR][1000 genomes]
rs7738592	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7745056	1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7750279	0.85[CEU][hapmap]
rs7750376	0.84[CEU][hapmap]
rs7754486	0.84[CEU][hapmap]
rs7756171	0.81[CEU][hapmap];0.92[CHB][hapmap]
rs7761372	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9483529	0.80[EUR][1000 genomes]
rs9483530	0.80[EUR][1000 genomes]
rs9493515	0.80[EUR][1000 genomes]
rs9493517	0.80[EUR][1000 genomes]
rs9493518	0.80[EUR][1000 genomes]
rs975225	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9791374	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][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	nsv532069	chr6:132776411-133462292	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv428154	chr6:133271975-133522803	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	esv3445931	chr6:133347824-133434532	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv519475	chr6:133350936-133474673	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4257872	BCLAF1	cis	parietal	SCAN
rs4257872	HBS1L	cis	parietal	SCAN
rs4257872	VNN2	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:133361200-133376200	Weak transcription	Psoas Muscle	Psoas
2	chr6:133368600-133376200	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr6:133371400-133376200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr6:133375600-133376600	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr6:133375800-133376400	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr6:133375800-133376400	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr6:133376000-133376800	Enhancers	H9 Cell Line	embryonic stem cell
8	chr6:133376000-133377400	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr6:133376000-133378000	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr6:133376000-133378000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:133376000-133378400	Enhancers	H1 Cell Line	embryonic stem cell

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