Variant report

Variant	rs4858713
Chromosome Location	chr3:19931752-19931753
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:19930446..19931966-chr3:19932163..19933731,2	MCF-7	breast:
2	chr3:19930434..19932349-chr3:19933276..19934867,2	K562	blood:
3	chr3:19930617..19933383-chr3:19987388..19990668,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144566	Chromatin interaction
ENSG00000163576	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10155054	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11925668	0.90[AFR][1000 genomes]
rs11927871	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13317268	0.90[AFR][1000 genomes]
rs17180771	0.91[ASN][1000 genomes]
rs17574049	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1872737	1.00[ASN][1000 genomes]
rs2101390	1.00[ASN][1000 genomes]
rs3849533	0.91[ASN][1000 genomes]
rs3916092	1.00[ASN][1000 genomes]
rs4858712	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858714	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55669125	0.91[ASN][1000 genomes]
rs55829813	1.00[ASN][1000 genomes]
rs56004950	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59572420	0.91[ASN][1000 genomes]
rs62279119	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62279120	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62279122	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62279123	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62279125	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62279132	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62279133	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62279134	1.00[ASN][1000 genomes]
rs62279135	1.00[ASN][1000 genomes]
rs62279136	1.00[ASN][1000 genomes]
rs62279138	1.00[ASN][1000 genomes]
rs6550213	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66526230	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73046020	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73188422	0.90[AFR][1000 genomes]
rs9809548	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9810613	0.91[ASN][1000 genomes]
rs9834480	0.81[AFR][1000 genomes]
rs9840739	0.81[AFR][1000 genomes]
rs9850665	0.81[AFR][1000 genomes]
rs9850795	0.87[AFR][1000 genomes]
rs9869783	0.87[AFR][1000 genomes]
rs9875453	0.90[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010123	chr3:18990307-19989504	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv433358	chr3:19547184-19996508	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	esv1828161	chr3:19547184-20062060	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer 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	17 gene(s)	inside rSNPs	diseases
4	esv1825914	chr3:19549859-20137270	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	esv1826570	chr3:19579860-20077414	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	esv1833139	chr3:19579860-20121349	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	17 gene(s)	inside rSNPs	diseases
8	esv1826254	chr3:19592688-20042834	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv1003183	chr3:19671647-19948351	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4858713	EFHB	cis	lung	GTEx

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:19927400-19941200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:19929600-19931800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr3:19930000-19932000	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr3:19930000-19932800	Enhancers	Fetal Stomach	stomach
5	chr3:19930400-19931800	Active TSS	Brain Anterior Caudate	brain
6	chr3:19930600-19931800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:19930600-19932400	Enhancers	Placenta	Placenta
8	chr3:19930600-19933200	Weak transcription	Gastric	stomach
9	chr3:19930800-19931800	Active TSS	Brain Cingulate Gyrus	brain
10	chr3:19930800-19931800	Active TSS	Brain Substantia Nigra	brain
11	chr3:19930800-19931800	Enhancers	HUVEC	blood vessel
12	chr3:19931000-19931800	Enhancers	K562	blood
13	chr3:19931000-19931800	Flanking Active TSS	Osteobl	bone
14	chr3:19931000-19932000	Weak transcription	Fetal Kidney	kidney
15	chr3:19931200-19931800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr3:19931200-19931800	Flanking Active TSS	Brain Hippocampus Middle	brain
17	chr3:19931200-19931800	Enhancers	Lung	lung
18	chr3:19931200-19933000	Weak transcription	HMEC	breast
19	chr3:19931400-19931800	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr3:19931400-19931800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr3:19931400-19931800	Weak transcription	Right Atrium	heart
22	chr3:19931400-19931800	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr3:19931400-19931800	Enhancers	Small Intestine	intestine
24	chr3:19931400-19931800	Flanking Active TSS	NHLF	lung
25	chr3:19931400-19932000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr3:19931400-19932000	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr3:19931400-19932600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:19931400-19932800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:19931400-19933200	Weak transcription	NH-A	brain
30	chr3:19931400-19933400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:19931400-19933800	Enhancers	NHDF-Ad	bronchial
32	chr3:19931400-19934000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr3:19931600-19931800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr3:19931600-19931800	Enhancers	Adipose Nuclei	Adipose
35	chr3:19931600-19931800	Enhancers	Duodenum Mucosa	Duodenum
36	chr3:19931600-19931800	Enhancers	Fetal Lung	lung
37	chr3:19931600-19932400	Enhancers	Rectal Mucosa Donor 29	rectum
38	chr3:19931600-19932400	Enhancers	A549	lung
39	chr3:19931600-19932600	Weak transcription	Colonic Mucosa	Colon
40	chr3:19931600-19933000	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr3:19931600-19933000	Weak transcription	NHEK	skin
42	chr3:19931600-19933200	Weak transcription	HSMM	muscle
43	chr3:19931600-19933800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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