Variant report

Variant	rs2330
Chromosome Location	chr3:139655773-139655774
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:139653263..139655437-chr3:139655759..139658179,2	K562	blood:

Variant related genes	Relation type
ENSG00000158258	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1426055	0.87[EUR][1000 genomes]
rs1834498	0.80[EUR][1000 genomes]
rs1834499	0.80[EUR][1000 genomes]
rs1834500	1.00[GIH][hapmap]
rs1834502	0.85[EUR][1000 genomes]
rs2349987	0.87[EUR][1000 genomes]
rs58528760	0.85[AMR][1000 genomes]
rs72979888	0.85[AMR][1000 genomes]
rs72979892	0.85[AMR][1000 genomes]
rs72979898	0.85[AMR][1000 genomes]
rs72979901	0.85[AMR][1000 genomes]
rs72981821	0.85[AMR][1000 genomes]
rs72981824	0.85[AMR][1000 genomes]
rs73870206	0.82[EUR][1000 genomes]
rs73870207	0.82[EUR][1000 genomes]
rs73870208	0.82[EUR][1000 genomes]
rs73870209	0.82[EUR][1000 genomes]
rs73870210	0.82[EUR][1000 genomes]
rs73870212	0.82[EUR][1000 genomes]
rs73870213	0.87[EUR][1000 genomes]
rs73870214	0.89[EUR][1000 genomes]
rs73870216	0.89[EUR][1000 genomes]
rs73870228	0.92[EUR][1000 genomes]
rs7610272	0.87[EUR][1000 genomes]
rs7611408	0.82[EUR][1000 genomes]
rs7633448	0.87[EUR][1000 genomes]
rs7649717	0.80[EUR][1000 genomes]
rs813100	0.87[EUR][1000 genomes]
rs9985239	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv916193	chr3:139187767-139821526	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv530058	chr3:139243971-139814419	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv998423	chr3:139526446-139947336	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv877544	chr3:139642572-139688415	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv3486576	chr3:139652862-139656260	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv3486577	chr3:139652862-139656260	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2330	MMP20	trans	lymphoblastoid	seeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139653200-139656000	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr3:139653400-139656200	Active TSS	Brain Angular Gyrus	brain
3	chr3:139653400-139657000	Active TSS	HSMMtube	muscle
4	chr3:139653600-139656600	Active TSS	Ovary	ovary
5	chr3:139655400-139656000	Bivalent Enhancer	Brain Germinal Matrix	brain
6	chr3:139655400-139656000	Bivalent Enhancer	Duodenum Mucosa	Duodenum
7	chr3:139655400-139656000	Bivalent/Poised TSS	NH-A	brain
8	chr3:139655400-139656200	Enhancers	Brain Anterior Caudate	brain
9	chr3:139655400-139656200	Bivalent Enhancer	Colon Smooth Muscle	Colon
10	chr3:139655600-139655800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:139655600-139655800	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:139655600-139655800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
13	chr3:139655600-139656000	Flanking Active TSS	Adipose Nuclei	Adipose
14	chr3:139655600-139656000	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
15	chr3:139655600-139656000	Bivalent Enhancer	Fetal Brain Male	brain
16	chr3:139655600-139656000	Bivalent/Poised TSS	Fetal Brain Female	brain
17	chr3:139655600-139656200	Enhancers	Pancreatic Islets	Pancreatic Islet
18	chr3:139655600-139658400	Weak transcription	Right Atrium	heart
19	chr3:139655600-139660400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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