Variant report

Variant	rs6533444
Chromosome Location	chr4:110561106-110561107
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:110555712..110559152-chr4:110560403..110563271,3	K562	blood:

Extended variants
information (count: 85 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10004377	0.83[LWK][hapmap]
rs10010159	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10017027	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10020263	0.95[CEU][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10032323	0.87[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs1008326	0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1029449	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1029450	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1029451	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1042891	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11098039	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11098040	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11724306	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11728699	0.82[LWK][hapmap]
rs11931318	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12498588	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12504296	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12504784	0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12511995	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12646055	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12647060	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13103167	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13112432	0.86[ASN][1000 genomes]
rs13151303	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1476545	0.88[GIH][hapmap]
rs2079131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2107050	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2107051	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2285712	0.95[CEU][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28380238	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28850086	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28892996	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3181187	0.83[LWK][hapmap]
rs3181191	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3182325	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34925690	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35838666	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733611	0.86[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3756256	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796911	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3796912	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4698744	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4698745	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4698747	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4698748	0.94[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4698776	0.81[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4698777	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4698780	0.86[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5030535	0.80[YRI][hapmap]
rs5030594	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5030606	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs59207576	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60916792	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6533438	0.81[CHD][hapmap];0.97[GIH][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6533445	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6815377	0.90[CEU][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6816926	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6825095	0.94[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6831930	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6833490	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6834082	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6834701	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6849691	0.90[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6851190	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6851356	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6856535	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs726583	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs726584	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs726585	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap]
rs735642	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7439493	0.88[LWK][hapmap]
rs763370	0.90[CEU][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7672819	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7674356	0.83[LWK][hapmap]
rs767598	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7694620	0.83[LWK][hapmap]
rs7699736	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7699969	0.81[TSI][hapmap];0.81[ASN][1000 genomes]
rs9990765	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9993532	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9996648	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9996730	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	nsv461613	chr4:109922064-110593460	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv595129	chr4:109922064-110593460	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3349784	chr4:110348873-110723163	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6533444	CASP6	cis	cerebellum	SCAN
rs6533444	COL25A1	cis	cerebellum	SCAN
rs6533444	LARP7	cis	parietal	SCAN
rs6533444	SGMS2	cis	cerebellum	SCAN
rs6533444	ANK2	cis	cerebellum	SCAN
rs6533444	CCDC109B	Cis_1M	lymphoblastoid	RTeQTL
rs6533444	CASP6	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110533000-110573000	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr4:110546200-110566400	Weak transcription	Fetal Thymus	thymus
3	chr4:110546600-110580600	Weak transcription	Thymus	Thymus
4	chr4:110550600-110569200	Weak transcription	GM12878-XiMat	blood
5	chr4:110553000-110565600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr4:110553200-110561600	Weak transcription	Primary B cells from peripheral blood	blood
7	chr4:110553200-110561800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr4:110553200-110565200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr4:110553200-110566200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr4:110553200-110566800	Weak transcription	Primary B cells from cord blood	blood
11	chr4:110553800-110562000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr4:110556800-110563000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr4:110559600-110562000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr4:110559600-110566600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr4:110559800-110562800	Weak transcription	Primary T cells from cord blood	blood
16	chr4:110560400-110561200	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr4:110560400-110564400	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr4:110560600-110561400	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr4:110560600-110564000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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