Variant report

Variant	rs13015243
Chromosome Location	chr2:55870697-55870698
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55865013..55867773-chr2:55869528..55871983,2	K562	blood:
2	chr2:55869282..55871288-chr2:55873763..55875349,2	MCF-7	breast:
3	chr2:55842502..55844882-chr2:55870584..55873430,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138041	Chromatin interaction
ENSG00000138035	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12623293	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12623937	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12987272	0.82[AMR][1000 genomes]
rs12993839	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12994656	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12998664	0.85[AMR][1000 genomes]
rs13001452	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13004436	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13007719	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13009649	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13014123	0.92[ASN][1000 genomes]
rs13025994	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13030396	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1542643	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs17737233	0.85[AMR][1000 genomes]
rs2054729	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34400247	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs35057183	0.88[AMR][1000 genomes]
rs35255044	0.83[AMR][1000 genomes]
rs35861320	0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs35968359	0.82[AMR][1000 genomes]
rs3748944	0.82[AMR][1000 genomes]
rs3748952	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6753530	0.82[AMR][1000 genomes]
rs878124	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	nsv1008452	chr2:55809191-55987274	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55846800-55919800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:55847400-55911000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:55847600-55886600	Weak transcription	Stomach Mucosa	stomach
4	chr2:55848000-55872600	Weak transcription	Small Intestine	intestine
5	chr2:55849200-55873200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr2:55849800-55882800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:55852000-55872400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr2:55853600-55882400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr2:55857000-55873800	Strong transcription	Fetal Thymus	thymus
10	chr2:55858200-55920400	Weak transcription	Fetal Heart	heart
11	chr2:55858600-55871600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr2:55858800-55873400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr2:55858800-55875600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr2:55858800-55877200	Strong transcription	Dnd41	blood
15	chr2:55859000-55876800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr2:55859000-55877000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr2:55859000-55877200	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr2:55859200-55874000	Weak transcription	Pancreas	Pancrea
19	chr2:55859400-55875600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:55859400-55877600	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr2:55859800-55871200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr2:55859800-55871400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr2:55859800-55873200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr2:55859800-55873600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr2:55860400-55905400	Weak transcription	Fetal Brain Male	brain
26	chr2:55860800-55871200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:55861800-55875000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr2:55861800-55875800	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr2:55862000-55873400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr2:55862000-55874800	Strong transcription	Fetal Muscle Trunk	muscle
31	chr2:55862000-55875000	Strong transcription	Fetal Intestine Large	intestine
32	chr2:55862000-55877200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr2:55862000-55877800	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr2:55862200-55871200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr2:55862200-55871200	Strong transcription	A549	lung
36	chr2:55862200-55871400	Strong transcription	GM12878-XiMat	blood
37	chr2:55862200-55873800	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr2:55862200-55874000	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr2:55862200-55874400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr2:55862200-55874800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr2:55862600-55871600	Strong transcription	Adipose Nuclei	Adipose
42	chr2:55863400-55871400	Strong transcription	Fetal Muscle Leg	muscle
43	chr2:55863400-55871400	Strong transcription	HepG2	liver
44	chr2:55863400-55875600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr2:55864000-55893200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr2:55864200-55882800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr2:55864400-55872400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr2:55864400-55919600	Weak transcription	NHLF	lung
49	chr2:55864600-55881400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr2:55864600-55881400	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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