Variant report

Variant	rs1357459
Chromosome Location	chr3:119514556-119514557
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119514298..119516694-chr3:119519777..119521864,2	K562	blood:
2	chr3:119513257..119518482-chr3:119518835..119521864,6	K562	blood:
3	chr3:119497497..119499606-chr3:119513242..119515425,2	K562	blood:
4	chr3:119512757..119515605-chr3:119516397..119518859,2	MCF-7	breast:
5	chr3:119215696..119217904-chr3:119512821..119515742,3	K562	blood:
6	chr3:119217125..119218663-chr3:119514473..119516155,2	K562	blood:

Variant related genes	Relation type
ENSG00000113845	Chromatin interaction
ENSG00000272662	Chromatin interaction
ENSG00000144852	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12492296	0.85[ASN][1000 genomes]
rs13059232	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13091204	0.92[ASN][1000 genomes]
rs1403526	0.90[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.89[ASN][1000 genomes]
rs2461817	0.86[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs2461821	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2461822	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2461823	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2472677	1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs4440154	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4688040	0.85[ASN][1000 genomes]
rs55764158	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6771638	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6772976	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011178	chr3:119437192-119589116	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv536703	chr3:119437192-119589116	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1357459	CCDC58	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119501800-119515000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:119512000-119515800	Genic enhancers	Fetal Intestine Small	intestine
3	chr3:119513400-119515000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr3:119513600-119514600	Enhancers	Adipose Nuclei	Adipose
5	chr3:119513600-119514800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:119513600-119515400	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr3:119513600-119515800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:119513800-119514600	Enhancers	Placenta	Placenta
9	chr3:119513800-119514800	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr3:119513800-119514800	Enhancers	Colonic Mucosa	Colon
11	chr3:119513800-119514800	Flanking Active TSS	Hela-S3	cervix
12	chr3:119513800-119514800	Enhancers	HSMMtube	muscle
13	chr3:119513800-119515000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:119513800-119515000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:119513800-119515200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:119513800-119515200	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr3:119513800-119515200	Flanking Active TSS	A549	lung
18	chr3:119513800-119515200	Flanking Active TSS	K562	blood
19	chr3:119513800-119516200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:119513800-119516200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:119513800-119516200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:119514000-119514600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr3:119514000-119514600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr3:119514000-119514600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr3:119514000-119514600	Enhancers	Gastric	stomach
26	chr3:119514000-119514600	Enhancers	Left Ventricle	heart
27	chr3:119514000-119514600	Enhancers	Placenta Amnion	Placenta Amnion
28	chr3:119514000-119514600	Enhancers	HSMM	muscle
29	chr3:119514000-119514600	Enhancers	HUVEC	blood vessel
30	chr3:119514000-119514800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr3:119514000-119514800	Enhancers	H9 Cell Line	embryonic stem cell
32	chr3:119514000-119514800	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr3:119514000-119514800	Flanking Active TSS	Liver	Liver
34	chr3:119514000-119515800	Flanking Active TSS	HepG2	liver
35	chr3:119514200-119514600	Flanking Active TSS	Fetal Intestine Large	intestine
36	chr3:119514200-119514800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
37	chr3:119514200-119515000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr3:119514200-119515000	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr3:119514200-119515800	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr3:119514200-119516000	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr3:119514400-119514600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:119514400-119514600	Weak transcription	Right Atrium	heart
43	chr3:119514400-119514600	Flanking Active TSS	Stomach Mucosa	stomach
44	chr3:119514400-119515000	Flanking Active TSS	Duodenum Mucosa	Duodenum
45	chr3:119514400-119515200	Enhancers	Small Intestine	intestine
46	chr3:119514400-119515400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
47	chr3:119514400-119516200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr3:119514400-119526800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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