Variant report

Variant	rs13128388
Chromosome Location	chr4:110568156-110568157
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:110566516..110569395-chr4:110734588..110736719,2	K562	blood:
2	chr4:110354508..110356666-chr4:110567789..110569544,2	K562	blood:
3	chr4:110568027..110570287-chr4:110582225..110584531,2	K562	blood:

Variant related genes	Relation type
ENSG00000138802	Chromatin interaction
ENSG00000247950	Chromatin interaction
ENSG00000272795	Chromatin interaction
ENSG00000109534	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1008327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11728573	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11734973	0.89[ASN][1000 genomes]
rs12513113	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13846	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1543812	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17440077	0.81[CEU][hapmap];0.84[JPT][hapmap];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2158204	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2346835	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28515508	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4698770	0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4698775	0.90[CEU][hapmap];0.93[CHB][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62326057	0.90[ASN][1000 genomes]
rs62326058	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62327660	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6533442	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6533446	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6824270	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]
rs6824542	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6858416	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72674829	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7658262	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7690921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13128388	CCDC109B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110533000-110573000	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr4:110546600-110580600	Weak transcription	Thymus	Thymus
3	chr4:110550600-110569200	Weak transcription	GM12878-XiMat	blood
4	chr4:110562400-110569000	Weak transcription	Primary B cells from peripheral blood	blood
5	chr4:110562800-110569400	Enhancers	Primary T cells from cord blood	blood
6	chr4:110564800-110568800	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr4:110564800-110569400	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr4:110565000-110569400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr4:110565200-110569400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
10	chr4:110565600-110569400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr4:110565800-110576600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:110566200-110568600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
13	chr4:110566200-110569400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr4:110566600-110569400	Enhancers	Primary T cells fromperipheralblood	blood
15	chr4:110566600-110569400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr4:110566800-110569600	Strong transcription	Primary B cells from cord blood	blood
17	chr4:110567000-110569400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr4:110567200-110568400	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr4:110567200-110570000	Weak transcription	Fetal Thymus	thymus
20	chr4:110567400-110570000	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr4:110567800-110568800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr4:110567800-110569000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr4:110567800-110570000	Weak transcription	HSMM	muscle
24	chr4:110568000-110568800	Enhancers	Primary T helper cells PMA-I stimulated	--

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