Variant report

Variant	rs2777907
Chromosome Location	chr1:179893120-179893121
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179890721..179893462-chr1:179922578..179925183,2	MCF-7	breast:
2	chr1:179862982..179865680-chr1:179892718..179895012,2	MCF-7	breast:
3	chr1:179892500..179895461-chr1:179925642..179927756,2	K562	blood:

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

Variant related genes	Relation type
ENSG00000260360	Chromatin interaction
ENSG00000135837	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1148813	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1148814	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1148816	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1281409	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1281414	0.81[ASN][1000 genomes]
rs1281415	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1281419	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1281431	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1295972	0.94[EUR][1000 genomes]
rs1299683	0.89[EUR][1000 genomes]
rs1299685	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17370666	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1758143	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2762857	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2777916	0.89[EUR][1000 genomes]
rs2794584	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs476280	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs524166	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs555755	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs576723	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs627897	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs651455	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs668813	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs683812	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179867400-179897200	Weak transcription	Stomach Mucosa	stomach
2	chr1:179887200-179893400	Weak transcription	Pancreas	Pancrea
3	chr1:179887200-179897200	Weak transcription	Fetal Intestine Small	intestine
4	chr1:179887400-179894600	Weak transcription	HSMMtube	muscle
5	chr1:179887400-179897200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:179887400-179897600	Weak transcription	Aorta	Aorta
7	chr1:179887400-179898600	Weak transcription	Right Ventricle	heart
8	chr1:179887400-179899200	Weak transcription	Small Intestine	intestine
9	chr1:179887400-179900600	Weak transcription	Ovary	ovary
10	chr1:179887400-179901600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr1:179887600-179895200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:179887600-179899400	Weak transcription	K562	blood
13	chr1:179887800-179899400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr1:179888000-179894600	Weak transcription	HMEC	breast
15	chr1:179888600-179895200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr1:179888600-179895600	Weak transcription	NHLF	lung
17	chr1:179888600-179897200	Weak transcription	Esophagus	oesophagus
18	chr1:179888600-179897200	Weak transcription	Fetal Intestine Large	intestine
19	chr1:179888600-179899400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr1:179888800-179894400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:179888800-179900600	Weak transcription	Adipose Nuclei	Adipose
22	chr1:179889000-179899400	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr1:179889200-179894200	Weak transcription	Hela-S3	cervix
24	chr1:179889200-179895000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr1:179889200-179899200	Weak transcription	HepG2	liver
26	chr1:179889600-179895000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:179889600-179895600	Weak transcription	NHDF-Ad	bronchial
28	chr1:179890200-179895400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr1:179890800-179893200	Weak transcription	Dnd41	blood
30	chr1:179890800-179893800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr1:179890800-179894600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:179891000-179895000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr1:179891000-179895000	Weak transcription	NHEK	skin
34	chr1:179891000-179895200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr1:179891000-179899200	Weak transcription	HUVEC	blood vessel
36	chr1:179891200-179893400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr1:179891200-179894000	Weak transcription	Left Ventricle	heart
38	chr1:179891200-179895600	Weak transcription	Placenta	Placenta
39	chr1:179891200-179899400	Weak transcription	GM12878-XiMat	blood
40	chr1:179891400-179893200	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr1:179891400-179893400	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr1:179891400-179893400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr1:179891400-179899400	Weak transcription	Liver	Liver
44	chr1:179891600-179893200	Weak transcription	Primary T cells from cord blood	blood
45	chr1:179891600-179893200	Weak transcription	Fetal Muscle Leg	muscle
46	chr1:179891600-179893200	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr1:179891600-179893400	Weak transcription	Primary B cells from peripheral blood	blood
48	chr1:179891600-179894400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr1:179891600-179894600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr1:179891600-179894600	Weak transcription	Osteobl	bone

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