Variant report

Variant	rs1076690
Chromosome Location	chr20:25655021-25655022
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SETDB1	chr20:25653876-25655064	U2OS	brain:	n/a	n/a
2	POLR2A	chr20:25655021-25655523	HepG2	liver:	n/a	n/a
3	POLR2A	chr20:25654927-25655104	MCF-7	breast:	n/a	n/a
4	POLR2A	chr20:25654971-25657550	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr20:25654914-25655692	PANC-1	pancreas:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25603937..25605836-chr20:25653672..25656998,3	MCF-7	breast:
2	chr20:25652247..25655467-chr20:25656048..25658706,3	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GINS1-1	chr20:25654488-25658710	ENSG00000213742.2

No data

Variant related genes	Relation type
MED28P7	TF binding region
ENSG00000170191	Chromatin interaction
ENSG00000213742	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs12106001	0.92[ASN][1000 genomes]
rs1891771	0.82[EUR][1000 genomes]
rs1936190	0.82[EUR][1000 genomes]
rs35516971	0.82[EUR][1000 genomes]
rs3813916	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4318454	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4368405	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58877578	0.88[AMR][1000 genomes]
rs59399848	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6037168	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6037192	0.90[ASN][1000 genomes]
rs6037196	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6037204	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6037206	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6037222	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs60463280	0.81[ASN][1000 genomes]
rs6050767	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6050770	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6050801	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6050805	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6050813	0.96[ASN][1000 genomes]
rs6050815	0.93[ASN][1000 genomes]
rs6050816	0.93[ASN][1000 genomes]
rs60897995	0.82[EUR][1000 genomes]
rs61052177	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61494938	0.82[EUR][1000 genomes]
rs66813885	0.82[EUR][1000 genomes]
rs66983770	0.82[EUR][1000 genomes]
rs7266592	0.80[AMR][1000 genomes]
rs7269064	0.83[EUR][1000 genomes]
rs73337394	0.80[AMR][1000 genomes]
rs73337401	0.80[AMR][1000 genomes]
rs73339323	0.88[AMR][1000 genomes]
rs73339360	0.88[AMR][1000 genomes]
rs73339379	0.88[AMR][1000 genomes]
rs73339383	0.88[AMR][1000 genomes]
rs73339387	0.88[AMR][1000 genomes]
rs73341305	0.84[EUR][1000 genomes]
rs73341314	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73341328	0.82[EUR][1000 genomes]
rs73341363	0.81[ASN][1000 genomes]
rs73341365	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73343275	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73343292	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73345249	0.82[EUR][1000 genomes]
rs73345278	0.82[EUR][1000 genomes]
rs73345286	0.82[EUR][1000 genomes]
rs73597829	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8125002	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912834	chr20:25615272-25756336	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1076690	RP4-694B14.5	cis	Thyroid	GTEx
rs1076690	RP4-694B14.5	cis	Adipose Subcutaneous	GTEx
rs1076690	ZNF337	cis	Thyroid	GTEx
rs1076690	ZNF337	cis	Adipose Subcutaneous	GTEx
rs1076690	ZNF337	cis	Stomach	GTEx
rs1076690	RP4-694B14.5	cis	Stomach	GTEx
rs1076690	RP4-694B14.5	cis	lung	GTEx
rs1076690	ZNF337	cis	lung	GTEx
rs1076690	NINL	cis	Nerve Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25625000-25655200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr20:25649200-25655200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr20:25650600-25655800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr20:25650600-25657000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr20:25651600-25659600	Strong transcription	Fetal Brain Female	brain
6	chr20:25651800-25655400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr20:25652000-25655600	Weak transcription	Fetal Heart	heart
8	chr20:25652000-25659600	Strong transcription	Brain Germinal Matrix	brain
9	chr20:25652600-25658800	Strong transcription	Fetal Stomach	stomach
10	chr20:25653000-25655200	Weak transcription	Hela-S3	cervix
11	chr20:25653000-25657000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr20:25653000-25663600	Strong transcription	HSMM	muscle
13	chr20:25653200-25655800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr20:25653200-25656800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr20:25653200-25657400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
16	chr20:25653200-25657400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr20:25653200-25659600	Strong transcription	Fetal Intestine Small	intestine
18	chr20:25653200-25662800	Strong transcription	Fetal Lung	lung
19	chr20:25653400-25656800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr20:25653400-25656800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr20:25653400-25656800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr20:25653400-25656800	Strong transcription	NH-A	brain
23	chr20:25653400-25657000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr20:25653400-25657400	Strong transcription	A549	lung
25	chr20:25653400-25657600	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr20:25653400-25657600	Strong transcription	Brain Substantia Nigra	brain
27	chr20:25653400-25657800	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr20:25653400-25658200	Strong transcription	Duodenum Mucosa	Duodenum
29	chr20:25653400-25658600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr20:25653400-25658800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr20:25653400-25659200	Strong transcription	Primary hematopoietic stem cells	blood
32	chr20:25653400-25659400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr20:25653400-25659600	Strong transcription	Brain Angular Gyrus	brain
34	chr20:25653400-25659600	Strong transcription	Fetal Muscle Trunk	muscle
35	chr20:25653400-25659600	Strong transcription	Ovary	ovary
36	chr20:25653400-25659600	Strong transcription	Skeletal Muscle Male	skeletal muscle
37	chr20:25653400-25659600	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr20:25653400-25661000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr20:25653400-25662400	Strong transcription	Liver	Liver
40	chr20:25653400-25663600	Strong transcription	Dnd41	blood
41	chr20:25653400-25664200	Strong transcription	Stomach Smooth Muscle	stomach
42	chr20:25653600-25655400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr20:25653600-25655600	Strong transcription	Adipose Nuclei	Adipose
44	chr20:25653600-25656600	Strong transcription	Brain Anterior Caudate	brain
45	chr20:25653600-25656800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr20:25653600-25657000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr20:25653600-25657000	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr20:25653600-25657000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr20:25653600-25657000	Strong transcription	HMEC	breast
50	chr20:25653600-25657000	Strong transcription	NHDF-Ad	bronchial

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