Variant report

Variant	rs4698876
Chromosome Location	chr4:103933567-103933568
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:103747371..103750739-chr4:103931209..103935255,4	MCF-7	breast:
2	chr4:103746101..103748655-chr4:103933460..103935226,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109332	Chromatin interaction
ENSG00000246560	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10006474	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10013062	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10516495	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10516496	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11929841	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11946020	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13150953	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13151569	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2866416	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34475639	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4698875	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4699048	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6533039	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6816370	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6843738	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7437975	0.82[ASN][1000 genomes]
rs7665026	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9991335	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757946	chr4:103780705-104057321	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2759270	chr4:103780705-104057321	ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv461598	chr4:103807720-103953389	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv594978	chr4:103807720-103953389	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv879684	chr4:103887561-103939894	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv3429917	chr4:103915319-104207455	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4698876	MANBA	cis	multi-tissue	Pritchard
rs4698876	MANBA	Cis_1M	lymphoblastoid	RTeQTL
rs4698876	BDH2	Cis_1M	lymphoblastoid	RTeQTL
rs4698876	KRT8P46	cis	lung	GTEx

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103930400-103934000	Enhancers	Fetal Heart	heart
2	chr4:103931600-103934200	Enhancers	Small Intestine	intestine
3	chr4:103931800-103934200	Enhancers	Duodenum Mucosa	Duodenum
4	chr4:103931800-103934200	Enhancers	Fetal Intestine Large	intestine
5	chr4:103931800-103934200	Enhancers	Fetal Intestine Small	intestine
6	chr4:103932000-103934000	Enhancers	Stomach Mucosa	stomach
7	chr4:103932200-103934000	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr4:103932400-103933600	Enhancers	HMEC	breast
9	chr4:103932400-103933800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:103932400-103933800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr4:103932400-103933800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr4:103932400-103933800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr4:103932400-103933800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr4:103932400-103933800	Enhancers	Stomach Smooth Muscle	stomach
15	chr4:103932400-103934000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr4:103932400-103934000	Enhancers	Ovary	ovary
17	chr4:103932400-103934000	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr4:103932400-103934000	Enhancers	NHEK	skin
19	chr4:103932400-103934200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr4:103932400-103934200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr4:103932400-103934200	Enhancers	K562	blood
22	chr4:103932400-103934400	Enhancers	Colon Smooth Muscle	Colon
23	chr4:103932400-103934400	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr4:103932400-103935600	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr4:103932600-103933600	Enhancers	HSMM	muscle
26	chr4:103932600-103933800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr4:103932600-103934000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr4:103932600-103934000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr4:103932600-103934000	Enhancers	Psoas Muscle	Psoas
30	chr4:103932600-103934000	Enhancers	HSMMtube	muscle
31	chr4:103932600-103934200	Enhancers	Rectal Smooth Muscle	rectum
32	chr4:103932600-103939600	Weak transcription	HepG2	liver
33	chr4:103932800-103933600	Enhancers	Rectal Mucosa Donor 29	rectum
34	chr4:103932800-103933600	Enhancers	NHDF-Ad	bronchial
35	chr4:103932800-103933800	Enhancers	Liver	Liver
36	chr4:103932800-103933800	Enhancers	Osteobl	bone
37	chr4:103932800-103934000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr4:103932800-103934000	Enhancers	Fetal Kidney	kidney
39	chr4:103932800-103934200	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr4:103932800-103934200	Enhancers	Adipose Nuclei	Adipose
41	chr4:103933000-103933600	Enhancers	NH-A	brain
42	chr4:103933000-103933800	Enhancers	Fetal Lung	lung
43	chr4:103933000-103934000	Enhancers	Muscle Satellite Cultured Cells	--
44	chr4:103933000-103934200	Enhancers	Brain Substantia Nigra	brain
45	chr4:103933000-103934600	Enhancers	Brain Anterior Caudate	brain
46	chr4:103933000-103934600	Enhancers	Hela-S3	cervix
47	chr4:103933000-103939600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr4:103933000-103940000	Weak transcription	Right Atrium	heart
49	chr4:103933200-103933600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
50	chr4:103933200-103934000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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