Variant report

Variant	rs1423652
Chromosome Location	chr5:42856350-42856351
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	chr5:42851174..42853504-chr5:42855107..42856666,2	K562	blood:
2	chr5:42853973..42857038-chr5:42873699..42877054,3	K562	blood:

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1035516	0.80[AMR][1000 genomes]
rs1046068	0.80[JPT][hapmap]
rs10941592	0.82[CEU][hapmap];0.91[MEX][hapmap]
rs10941593	0.82[CEU][hapmap]
rs11952526	0.84[CEU][hapmap]
rs11953554	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11958761	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12187996	0.80[JPT][hapmap]
rs12517112	0.80[JPT][hapmap]
rs12519532	0.82[CEU][hapmap]
rs12520759	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12521615	0.82[CEU][hapmap];0.91[MEX][hapmap]
rs12522458	0.82[AMR][1000 genomes]
rs1423649	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1423651	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2113086	0.82[CEU][hapmap];0.84[AMR][1000 genomes]
rs2161600	0.82[AMR][1000 genomes]
rs28919892	0.80[JPT][hapmap];0.91[MEX][hapmap]
rs35896631	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3797310	0.80[JPT][hapmap]
rs3849695	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4866799	0.80[AMR][1000 genomes]
rs4866803	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4866804	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4866805	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4866806	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4866949	0.83[JPT][hapmap]
rs4866967	0.84[AMR][1000 genomes]
rs55687632	0.84[AMR][1000 genomes]
rs55688895	0.84[AMR][1000 genomes]
rs58394380	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59073137	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61099053	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61371942	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62370951	0.80[AMR][1000 genomes]
rs62370953	0.80[AMR][1000 genomes]
rs62370959	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6865453	0.82[CEU][hapmap]
rs6880056	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6882786	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6896902	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7579	0.80[JPT][hapmap];0.91[MEX][hapmap]
rs7703376	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7708223	0.80[JPT][hapmap]
rs7719242	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7725776	0.80[JPT][hapmap]
rs7725961	0.85[CEU][hapmap]
rs7730190	0.80[JPT][hapmap]
rs7734918	0.81[CEU][hapmap]
rs7735857	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs882775	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9687651	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
2	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases
3	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
4	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
5	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
6	nsv523033	chr5:42752037-42919685	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv965602	chr5:42767568-42889585	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
9	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
10	nsv534185	chr5:42804840-43067088	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	165 gene(s)	inside rSNPs	diseases
11	nsv1018276	chr5:42809131-42975245	Strong transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1423652	CCDC152	cis	Artery Tibial	GTEx
rs1423652	OXCT1	cis	parietal	SCAN
rs1423652	CCDC152	cis	Artery Aorta	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42851400-42858400	Enhancers	HepG2	liver
2	chr5:42853200-42858400	Enhancers	Brain Substantia Nigra	brain
3	chr5:42853400-42858400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr5:42854000-42856600	Enhancers	Liver	Liver
5	chr5:42854000-42857800	Enhancers	Brain Hippocampus Middle	brain
6	chr5:42854200-42858400	Weak transcription	K562	blood
7	chr5:42855000-42857000	Enhancers	Fetal Lung	lung
8	chr5:42855000-42857800	Enhancers	Brain Angular Gyrus	brain
9	chr5:42855000-42858400	Enhancers	Brain Anterior Caudate	brain
10	chr5:42855000-42859200	Enhancers	HSMM	muscle
11	chr5:42855200-42856800	Enhancers	Fetal Intestine Small	intestine
12	chr5:42855200-42857400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr5:42855200-42858200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr5:42855200-42859600	Enhancers	Fetal Intestine Large	intestine
15	chr5:42855600-42858200	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr5:42855800-42857400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr5:42855800-42858200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr5:42855800-42858400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr5:42855800-42858800	Weak transcription	Duodenum Mucosa	Duodenum
20	chr5:42856000-42858200	Weak transcription	HSMMtube	muscle
21	chr5:42856200-42857200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr5:42856200-42857200	Weak transcription	Left Ventricle	heart
23	chr5:42856200-42857400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr5:42856200-42857600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr5:42856200-42858200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr5:42856200-42858200	Weak transcription	Osteobl	bone
27	chr5:42856200-42858400	Weak transcription	Psoas Muscle	Psoas
28	chr5:42856200-42858400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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