Variant report

Variant	rs73940017
Chromosome Location	chr2:55748319-55748320
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55746181..55748765-chr2:55843177..55845713,3	MCF-7	breast:
2	chr2:55645285..55648583-chr2:55744780..55749543,7	K562	blood:
3	chr2:55728050..55729964-chr2:55747020..55749706,2	MCF-7	breast:
4	chr2:55747318..55749114-chr2:55750754..55752618,2	MCF-7	breast:
5	chr2:55494907..55497145-chr2:55746886..55748961,2	MCF-7	breast:
6	chr2:55734348..55736732-chr2:55747645..55749289,2	K562	blood:
7	chr2:55746965..55749333-chr2:55759467..55761461,2	K562	blood:

Variant related genes	Relation type
ENSG00000115355	Chromatin interaction
ENSG00000085760	Chromatin interaction
ENSG00000272606	Chromatin interaction
ENSG00000138041	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10496046	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17736028	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17736159	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17736300	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17744287	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17744399	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17792467	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17792539	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17792972	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35232864	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3748950	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56043131	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56079154	0.84[AFR][1000 genomes]
rs56098806	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs59722606	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60555175	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73940015	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73940018	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73942925	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv874160	chr2:55713102-55828974	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv525434	chr2:55716650-55841640	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv834080	chr2:55741036-55927928	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
7	esv2757798	chr2:55747239-55981074	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	esv2759050	chr2:55747239-55981074	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55745800-55748400	Active TSS	Brain Anterior Caudate	brain
2	chr2:55745800-55748400	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr2:55747000-55748600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr2:55747200-55748400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:55747200-55748400	Flanking Active TSS	Dnd41	blood
6	chr2:55747600-55748400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr2:55747600-55748400	Flanking Active TSS	Hela-S3	cervix
8	chr2:55747600-55752200	Weak transcription	Lung	lung
9	chr2:55747600-55753000	Weak transcription	Spleen	Spleen
10	chr2:55747800-55751000	Weak transcription	Fetal Muscle Trunk	muscle
11	chr2:55747800-55751200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:55747800-55751400	Weak transcription	Pancreas	Pancrea
13	chr2:55747800-55752000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:55747800-55752800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:55747800-55753600	Weak transcription	Gastric	stomach
16	chr2:55747800-55784000	Weak transcription	Esophagus	oesophagus
17	chr2:55748000-55748400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:55748000-55748400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:55748000-55748400	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr2:55748000-55748400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr2:55748000-55748400	Enhancers	Adipose Nuclei	Adipose
22	chr2:55748000-55748600	Enhancers	Primary T cells fromperipheralblood	blood
23	chr2:55748000-55748600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr2:55748000-55748600	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr2:55748000-55748600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr2:55748000-55749600	Weak transcription	Fetal Stomach	stomach
27	chr2:55748000-55750000	Weak transcription	Left Ventricle	heart
28	chr2:55748000-55751400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr2:55748000-55751600	Weak transcription	Liver	Liver
30	chr2:55748000-55752000	Weak transcription	Stomach Mucosa	stomach
31	chr2:55748000-55752200	Weak transcription	Placenta	Placenta
32	chr2:55748000-55752200	Weak transcription	Ovary	ovary
33	chr2:55748000-55752200	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr2:55748000-55752200	Weak transcription	Right Ventricle	heart
35	chr2:55748000-55752400	Weak transcription	Aorta	Aorta
36	chr2:55748000-55753000	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr2:55748000-55757600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr2:55748000-55761200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr2:55748000-55761200	Weak transcription	Primary B cells from cord blood	blood
40	chr2:55748000-55784000	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr2:55748000-55788000	Weak transcription	Colonic Mucosa	Colon
42	chr2:55748000-55793800	Weak transcription	Psoas Muscle	Psoas
43	chr2:55748200-55748400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr2:55748200-55748400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr2:55748200-55748400	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr2:55748200-55748400	Enhancers	Brain Substantia Nigra	brain
47	chr2:55748200-55748400	Enhancers	A549	lung
48	chr2:55748200-55748400	Active TSS	GM12878-XiMat	blood
49	chr2:55748200-55748400	Enhancers	HepG2	liver
50	chr2:55748200-55748400	Active TSS	HMEC	breast

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