Variant report

Variant	rs2777909
Chromosome Location	chr1:179893810-179893811
allele	C/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:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:179850807..179852976-chr1:179893272..179895971,2	MCF-7	breast:
2	chr1:179893782..179897328-chr1:179897862..179901956,4	MCF-7	breast:
3	chr1:179884044..179886967-chr1:179893191..179895290,2	K562	blood:
4	chr1:179862982..179865680-chr1:179892718..179895012,2	MCF-7	breast:
5	chr1:179892500..179895461-chr1:179925642..179927756,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TOR1AIP1-3	chr1:179891690-179894128	NONHSAT008230

No data

Variant related genes	Relation type
ENSG00000272906	Chromatin interaction
ENSG00000143337	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1144575	0.93[ASN][1000 genomes]
rs1148812	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1148815	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12062341	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12062383	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1281378	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1281408	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1281411	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1281412	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1281413	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1281428	0.91[ASN][1000 genomes]
rs1281429	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1281430	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1281432	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1298477	0.83[AMR][1000 genomes]
rs1298479	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1300068	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2007148	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2245425	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2249346	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2762858	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2777908	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2777917	0.87[AMR][1000 genomes]
rs2794582	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2794583	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs474258	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs475233	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs475434	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs479094	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs480377	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs480498	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs486906	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs501300	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs505789	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs505837	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs507603	0.94[ASN][1000 genomes]
rs514421	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs518774	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs522534	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs530369	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs530854	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs538512	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs547776	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs549650	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs553830	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs555270	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs555526	0.95[ASN][1000 genomes]
rs589780	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs599185	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs600046	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs600553	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs605807	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs609521	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs612215	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs644412	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv429947	chr1:179790518-179925104	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179867400-179897200	Weak transcription	Stomach Mucosa	stomach
2	chr1:179887200-179897200	Weak transcription	Fetal Intestine Small	intestine
3	chr1:179887400-179894600	Weak transcription	HSMMtube	muscle
4	chr1:179887400-179897200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:179887400-179897600	Weak transcription	Aorta	Aorta
6	chr1:179887400-179898600	Weak transcription	Right Ventricle	heart
7	chr1:179887400-179899200	Weak transcription	Small Intestine	intestine
8	chr1:179887400-179900600	Weak transcription	Ovary	ovary
9	chr1:179887400-179901600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr1:179887600-179895200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:179887600-179899400	Weak transcription	K562	blood
12	chr1:179887800-179899400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr1:179888000-179894600	Weak transcription	HMEC	breast
14	chr1:179888600-179895200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:179888600-179895600	Weak transcription	NHLF	lung
16	chr1:179888600-179897200	Weak transcription	Esophagus	oesophagus
17	chr1:179888600-179897200	Weak transcription	Fetal Intestine Large	intestine
18	chr1:179888600-179899400	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr1:179888800-179894400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:179888800-179900600	Weak transcription	Adipose Nuclei	Adipose
21	chr1:179889000-179899400	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr1:179889200-179894200	Weak transcription	Hela-S3	cervix
23	chr1:179889200-179895000	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr1:179889200-179899200	Weak transcription	HepG2	liver
25	chr1:179889600-179895000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:179889600-179895600	Weak transcription	NHDF-Ad	bronchial
27	chr1:179890200-179895400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:179890800-179894600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:179891000-179895000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:179891000-179895000	Weak transcription	NHEK	skin
31	chr1:179891000-179895200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr1:179891000-179899200	Weak transcription	HUVEC	blood vessel
33	chr1:179891200-179894000	Weak transcription	Left Ventricle	heart
34	chr1:179891200-179895600	Weak transcription	Placenta	Placenta
35	chr1:179891200-179899400	Weak transcription	GM12878-XiMat	blood
36	chr1:179891400-179899400	Weak transcription	Liver	Liver
37	chr1:179891600-179894400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr1:179891600-179894600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr1:179891600-179894600	Weak transcription	Osteobl	bone
40	chr1:179891600-179895400	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr1:179891600-179899600	Weak transcription	Duodenum Mucosa	Duodenum
42	chr1:179891800-179894000	Weak transcription	Psoas Muscle	Psoas
43	chr1:179892000-179894400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:179892000-179895400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr1:179892400-179894400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr1:179893000-179895000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr1:179893800-179894600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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