Variant report

Variant	rs343164
Chromosome Location	chr2:20579705-20579706
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:20577593..20583526-chr2:20584013..20588692,7	MCF-7	breast:
2	chr2:20573304..20576530-chr2:20577907..20583085,5	MCF-7	breast:
3	chr2:20579020..20581458-chr2:20591808..20594214,2	MCF-7	breast:
4	chr2:20558156..20560434-chr2:20578945..20580721,2	MCF-7	breast:
5	chr2:20578892..20581003-chr2:20669683..20672466,2	MCF-7	breast:
6	chr2:20578207..20580776-chr2:20580974..20582727,2	MCF-7	breast:
7	chr2:20565193..20568010-chr2:20578320..20581301,2	MCF-7	breast:
8	chr2:20571196..20572728-chr2:20579213..20580832,2	MCF-7	breast:
9	chr2:20578802..20580924-chr2:20708669..20710555,2	MCF-7	breast:
10	chr2:20549182..20552986-chr2:20577851..20580428,3	K562	blood:
11	chr2:20577324..20583172-chr2:20644517..20653341,20	MCF-7	breast:

No data

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

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10190763	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11096655	1.00[CEU][hapmap];0.83[CHB][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11679966	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11683916	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11686919	0.83[EUR][1000 genomes]
rs2110409	1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2160072	0.88[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2348704	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs343163	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs343165	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3771228	0.95[CEU][hapmap]
rs4666299	0.85[EUR][1000 genomes]
rs4666304	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4666305	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4666382	1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4666383	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6531232	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6713329	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6754782	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6756819	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7355288	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7596797	0.83[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:60 , 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	chr2:20578200-20581200	Enhancers	Fetal Muscle Trunk	muscle
3	chr2:20578400-20579800	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr2:20578600-20580800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:20578800-20579800	Enhancers	Brain Cingulate Gyrus	brain
6	chr2:20578800-20579800	Enhancers	Brain Substantia Nigra	brain
7	chr2:20579000-20581200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr2:20579000-20581200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr2:20579000-20581200	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr2:20579200-20580600	Weak transcription	Brain Germinal Matrix	brain
11	chr2:20579200-20580600	Weak transcription	Placenta	Placenta
12	chr2:20579200-20580800	Weak transcription	Right Atrium	heart
13	chr2:20579200-20581200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr2:20579200-20581200	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr2:20579200-20581200	Weak transcription	Liver	Liver
16	chr2:20579200-20581400	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr2:20579200-20582400	Weak transcription	A549	lung
18	chr2:20579200-20582600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:20579200-20583000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr2:20579200-20583000	Weak transcription	HSMM	muscle
21	chr2:20579200-20583200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr2:20579200-20585400	Weak transcription	Colonic Mucosa	Colon
23	chr2:20579400-20579800	Enhancers	Rectal Smooth Muscle	rectum
24	chr2:20579400-20580400	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr2:20579400-20580400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr2:20579400-20580400	Weak transcription	Brain Hippocampus Middle	brain
27	chr2:20579400-20580600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr2:20579400-20580600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr2:20579400-20580600	Weak transcription	Fetal Intestine Large	intestine
30	chr2:20579400-20580600	Weak transcription	Fetal Intestine Small	intestine
31	chr2:20579400-20580600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr2:20579400-20581000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:20579400-20581000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:20579400-20581000	Weak transcription	Brain Anterior Caudate	brain
35	chr2:20579400-20581000	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr2:20579400-20581000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr2:20579400-20581200	Weak transcription	Duodenum Mucosa	Duodenum
38	chr2:20579400-20581200	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr2:20579400-20581200	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr2:20579400-20581200	Weak transcription	K562	blood
41	chr2:20579400-20581200	Weak transcription	NH-A	brain
42	chr2:20579400-20581200	Weak transcription	NHLF	lung
43	chr2:20579400-20581600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr2:20579400-20581800	Weak transcription	Fetal Brain Male	brain
45	chr2:20579400-20583000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr2:20579400-20584600	Weak transcription	Small Intestine	intestine
47	chr2:20579400-20585000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr2:20579400-20586000	Weak transcription	NHDF-Ad	bronchial
49	chr2:20579400-20586200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr2:20579400-20586200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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