Variant report

Variant	rs6858416
Chromosome Location	chr4:110570991-110570992
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CASP6-3	chr4:110570571-110571385	ucscGeneNc_uc003hzj_2

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1008327	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11734973	0.84[ASN][1000 genomes]
rs12513113	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13128388	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13846	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1543812	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2158204	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2346835	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4698770	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4698775	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62326057	0.85[ASN][1000 genomes]
rs62326058	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62327660	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6533442	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6533446	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6824270	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6824542	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6857252	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72674829	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7658262	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7690921	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[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
rs6858416	CCDC109B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:27 , 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	chr4:110565800-110576600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:110568400-110573600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr4:110569400-110571200	Flanking Active TSS	GM12878-XiMat	blood
6	chr4:110569600-110572200	Weak transcription	Primary B cells from cord blood	blood
7	chr4:110569800-110571400	ZNF genes & repeats	Dnd41	blood
8	chr4:110569800-110573200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr4:110569800-110573200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr4:110570000-110571400	Strong transcription	Fetal Thymus	thymus
11	chr4:110570000-110571600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
12	chr4:110570000-110572600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr4:110570200-110571200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
14	chr4:110570400-110571400	Enhancers	Primary T cells fromperipheralblood	blood
15	chr4:110570400-110573200	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr4:110570400-110582000	Weak transcription	HSMM	muscle
17	chr4:110570600-110571000	Enhancers	Primary T cells from cord blood	blood
18	chr4:110570600-110571000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr4:110570600-110571000	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr4:110570600-110572200	Weak transcription	Primary B cells from peripheral blood	blood
21	chr4:110570600-110572400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr4:110570600-110573000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr4:110570800-110571000	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr4:110570800-110571200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr4:110570800-110572200	Weak transcription	Primary hematopoietic stem cells	blood
26	chr4:110570800-110572400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr4:110570800-110573600	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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