Variant report

Variant	rs2234679
Chromosome Location	chr2:113875584-113875585
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:113863108..113865660-chr2:113875310..113877504,3	MCF-7	breast:
2	chr2:113874258..113877773-chr2:113883397..113886122,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PSD4-5	chr2:113875558-113875605	NONHSAT073743

Variant related genes	Relation type
ENSG00000136689	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11677397	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs128964	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16065	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1794065	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1794067	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1794068	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2234676	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2234677	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2234678	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2853628	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs315933	0.81[EUR][1000 genomes]
rs315936	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs392503	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs408392	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs419598	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs423904	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4251967	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4251968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4251969	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4251970	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4251974	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4251975	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4251976	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4251977	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4251978	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4251979	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4251980	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4251981	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4251983	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4251984	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4251985	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4251986	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs431726	0.89[EUR][1000 genomes]
rs432014	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs434792	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs440286	0.80[AMR][1000 genomes]
rs442710	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs444413	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs446433	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs447713	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs448341	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs451578	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs454078	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs495282	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs495410	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs598859	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs878972	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997348	chr2:113688093-113986508	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1007254	chr2:113726982-113887782	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv535894	chr2:113726982-113887782	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv1003928	chr2:113846503-113887782	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv979338	chr2:113869830-113880320	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv874895	chr2:113870663-113875892	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv874896	chr2:113874122-113875892	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113872600-113875600	Enhancers	Primary B cells from peripheral blood	blood
2	chr2:113873000-113875600	Enhancers	Primary hematopoietic stem cells	blood
3	chr2:113873000-113875600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr2:113873200-113876000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr2:113873400-113875600	Enhancers	Duodenum Mucosa	Duodenum
6	chr2:113873600-113876000	Enhancers	Placenta Amnion	Placenta Amnion
7	chr2:113873600-113876000	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr2:113874000-113875600	Enhancers	HMEC	breast
9	chr2:113874200-113876000	Enhancers	NHDF-Ad	bronchial
10	chr2:113874200-113877200	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr2:113874400-113875600	Enhancers	Monocytes-CD14+_RO01746	blood
12	chr2:113874400-113875800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:113874400-113875800	Enhancers	Fetal Muscle Leg	muscle
14	chr2:113874400-113877000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr2:113874600-113875800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:113874600-113876000	Enhancers	K562	blood
17	chr2:113874600-113877600	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr2:113874600-113878400	Weak transcription	GM12878-XiMat	blood
19	chr2:113874800-113875600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr2:113874800-113875600	Enhancers	Osteobl	bone
21	chr2:113874800-113875800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:113874800-113875800	Enhancers	NH-A	brain
23	chr2:113874800-113878800	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr2:113875000-113875800	Enhancers	Lung	lung
25	chr2:113875000-113877000	Weak transcription	Small Intestine	intestine
26	chr2:113875000-113878600	Active TSS	Esophagus	oesophagus
27	chr2:113875200-113875600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
28	chr2:113875200-113875800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr2:113875200-113875800	Enhancers	Fetal Brain Male	brain
30	chr2:113875400-113875600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr2:113875400-113875800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr2:113875400-113875800	Enhancers	Placenta	Placenta
33	chr2:113875400-113875800	Enhancers	Pancreas	Pancrea
34	chr2:113875400-113875800	Flanking Active TSS	Stomach Mucosa	stomach
35	chr2:113875400-113875800	Enhancers	Hela-S3	cervix
36	chr2:113875400-113876000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:113875400-113876000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr2:113875400-113876000	Enhancers	Gastric	stomach
39	chr2:113875400-113876200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr2:113875400-113876200	Flanking Active TSS	NHEK	skin
41	chr2:113875400-113876600	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr2:113875400-113887400	Weak transcription	Spleen	Spleen

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