Variant report

Variant	rs6824270
Chromosome Location	chr4:110573339-110573340
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	chr4:110343302..110344212-chr4:110573149..110574182,3	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1008327	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11734973	0.83[ASN][1000 genomes]
rs12513113	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13128388	0.85[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13846	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1543812	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17440077	0.82[CHD][hapmap];0.80[GIH][hapmap];0.84[JPT][hapmap]
rs2158204	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2346835	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4698770	0.80[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4698775	0.80[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62326057	0.83[ASN][1000 genomes]
rs62326058	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62327660	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6533442	0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6533446	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6824542	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6857252	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6858416	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72674829	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7658262	1.00[CEU][hapmap];0.80[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7690921	1.00[ASW][hapmap];0.85[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.82[MEX][hapmap];0.92[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6824270	CCDC109B	Cis_1M	lymphoblastoid	RTeQTL
rs6824270	CASP6	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110546600-110580600	Weak transcription	Thymus	Thymus
2	chr4:110565800-110576600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:110568400-110573600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr4:110570400-110582000	Weak transcription	HSMM	muscle
5	chr4:110570800-110573600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr4:110571000-110605400	Weak transcription	Left Ventricle	heart
7	chr4:110571200-110573400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr4:110571200-110573400	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr4:110571200-110573600	Enhancers	Primary T cells from cord blood	blood
10	chr4:110571200-110573600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr4:110571200-110573800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr4:110571400-110573600	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr4:110571400-110573600	Weak transcription	Fetal Thymus	thymus
14	chr4:110572200-110574200	ZNF genes & repeats	Primary B cells from cord blood	blood
15	chr4:110572200-110574200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
16	chr4:110572400-110574600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr4:110572600-110576800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr4:110572600-110623200	Weak transcription	Esophagus	oesophagus
19	chr4:110573000-110573600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr4:110573000-110574200	ZNF genes & repeats	Primary B cells from peripheral blood	blood
21	chr4:110573000-110574200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
22	chr4:110573000-110574200	ZNF genes & repeats	Dnd41	blood
23	chr4:110573000-110574200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
24	chr4:110573200-110573400	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr4:110573200-110573400	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr4:110573200-110573600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr4:110573200-110573800	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr4:110573200-110574200	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr4:110573200-110574200	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
30	chr4:110573200-110588200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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