Variant report

Variant	rs343165
Chromosome Location	chr2:20578805-20578806
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:20525636..20526172-chr2:20578625..20579319,2	MCF-7	breast:
2	chr2:20577593..20583526-chr2:20584013..20588692,7	MCF-7	breast:
3	chr2:20268380..20271374-chr2:20576831..20579270,2	MCF-7	breast:
4	chr2:20573304..20576530-chr2:20577907..20583085,5	MCF-7	breast:
5	chr2:20551173..20551947-chr2:20578423..20578988,3	MCF-7	breast:
6	chr2:20578609..20579250-chr2:20646643..20647374,2	MCF-7	breast:
7	chr2:20551173..20551919-chr2:20578436..20578988,2	MCF-7	breast:
8	chr2:20578207..20580776-chr2:20580974..20582727,2	MCF-7	breast:
9	chr2:20565193..20568010-chr2:20578320..20581301,2	MCF-7	breast:
10	chr2:20578802..20580924-chr2:20708669..20710555,2	MCF-7	breast:
11	chr2:20549182..20552986-chr2:20577851..20580428,3	K562	blood:
12	chr2:20578457..20578968-chr2:20876175..20876882,2	MCF-7	breast:
13	chr2:20577324..20583172-chr2:20644517..20653341,20	MCF-7	breast:
14	chr2:20578184..20579084-chr2:20674706..20675486,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000228950	Chromatin interaction
ENSG00000055917	Chromatin interaction
ENSG00000232800	Chromatin interaction
ENSG00000143878	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10190763	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11096655	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11679966	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11683916	0.90[EUR][1000 genomes]
rs11686919	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2110409	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2160072	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2348704	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs343163	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs343164	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4666299	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4666304	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4666305	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4666382	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4666383	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6531232	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6713329	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6754782	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6756819	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7355288	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7596797	0.93[AMR][1000 genomes];0.91[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	nsv873716	chr2:20572094-20621404	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20575400-20581000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr2:20577200-20579600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr2:20577800-20579600	Enhancers	Fetal Muscle Leg	muscle
4	chr2:20578000-20579400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:20578000-20579400	Flanking Bivalent TSS/Enh	HepG2	liver
6	chr2:20578200-20579000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr2:20578200-20579200	Enhancers	Placenta	Placenta
8	chr2:20578200-20579400	Enhancers	Fetal Intestine Large	intestine
9	chr2:20578200-20579600	Enhancers	Fetal Heart	heart
10	chr2:20578200-20579600	Enhancers	Fetal Lung	lung
11	chr2:20578200-20581200	Enhancers	Fetal Muscle Trunk	muscle
12	chr2:20578400-20579000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr2:20578400-20579000	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr2:20578400-20579400	Enhancers	Duodenum Smooth Muscle	Duodenum
15	chr2:20578400-20579400	Enhancers	Fetal Brain Male	brain
16	chr2:20578400-20579400	Enhancers	HSMMtube	muscle
17	chr2:20578400-20579400	Enhancers	K562	blood
18	chr2:20578400-20579600	Enhancers	Colon Smooth Muscle	Colon
19	chr2:20578400-20579600	Enhancers	Fetal Stomach	stomach
20	chr2:20578400-20579800	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr2:20578600-20579000	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr2:20578600-20579000	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr2:20578600-20579000	Enhancers	Fetal Kidney	kidney
24	chr2:20578600-20579200	Enhancers	H1 Cell Line	embryonic stem cell
25	chr2:20578600-20579200	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr2:20578600-20579200	Enhancers	Right Atrium	heart
27	chr2:20578600-20579200	Enhancers	A549	lung
28	chr2:20578600-20579200	Enhancers	HSMM	muscle
29	chr2:20578600-20579400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:20578600-20579400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:20578600-20579400	Enhancers	Muscle Satellite Cultured Cells	--
32	chr2:20578600-20579400	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr2:20578600-20579400	Enhancers	Duodenum Mucosa	Duodenum
34	chr2:20578600-20579400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr2:20578600-20579400	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr2:20578600-20579400	Enhancers	HMEC	breast
37	chr2:20578600-20579400	Enhancers	NHLF	lung
38	chr2:20578600-20579600	Enhancers	Left Ventricle	heart
39	chr2:20578600-20579600	Enhancers	Ovary	ovary
40	chr2:20578600-20580800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr2:20578800-20579000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr2:20578800-20579000	Enhancers	Aorta	Aorta
43	chr2:20578800-20579000	Flanking Active TSS	Rectal Smooth Muscle	rectum
44	chr2:20578800-20579200	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:20578800-20579200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr2:20578800-20579200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr2:20578800-20579200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr2:20578800-20579200	Enhancers	Liver	Liver
49	chr2:20578800-20579200	Enhancers	Brain Germinal Matrix	brain
50	chr2:20578800-20579200	Enhancers	Pancreas	Pancrea

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