Variant report

Variant	rs72888489
Chromosome Location	chr2:183901438-183901439
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:183899689..183901875-chr2:183913168..183915328,2	K562	blood:
2	chr2:183860715..183863358-chr2:183901045..183903186,2	K562	blood:
3	chr2:183897885..183903273-chr2:183986817..183992325,13	K562	blood:
4	chr2:183900058..183902325-chr2:183948549..183950456,2	K562	blood:
5	chr2:183895298..183904606-chr2:183986062..183992067,16	K562	blood:
6	chr2:183871994..183874914-chr2:183897971..183902484,5	MCF-7	breast:
7	chr2:183899076..183901468-chr2:183926416..183929054,2	MCF-7	breast:
8	chr2:183900414..183906188-chr2:183987961..183990917,10	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000163002	Chromatin interaction

Extended variants
information (count: 132 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs1473614	0.86[EUR][1000 genomes]
rs1473615	0.86[EUR][1000 genomes]
rs1473616	0.86[EUR][1000 genomes]
rs2675054	0.86[EUR][1000 genomes]
rs2705715	0.86[EUR][1000 genomes]
rs2705718	0.86[EUR][1000 genomes]
rs2705719	0.86[EUR][1000 genomes]
rs2705720	0.86[EUR][1000 genomes]
rs2705721	0.86[EUR][1000 genomes]
rs35142583	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs36077496	0.87[AMR][1000 genomes]
rs55657876	0.86[EUR][1000 genomes]
rs55696219	0.86[EUR][1000 genomes]
rs55707150	0.86[EUR][1000 genomes]
rs55764044	0.86[EUR][1000 genomes]
rs55957340	0.86[EUR][1000 genomes]
rs56152140	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56182353	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6707761	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6712479	0.86[EUR][1000 genomes]
rs6722457	0.86[EUR][1000 genomes]
rs6743323	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6750392	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72886518	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72886527	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72886538	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72886541	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72886545	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72886547	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72886553	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72886557	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72886568	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72886577	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72886596	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72886600	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72888431	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72888449	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72888452	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72888461	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72888464	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72888472	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72888474	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72888478	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72888481	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72888488	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72890307	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72890345	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72890349	1.00[AMR][1000 genomes]
rs72890352	0.87[AMR][1000 genomes]
rs72890353	0.87[AMR][1000 genomes]
rs72890370	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72890384	0.87[AMR][1000 genomes]
rs72890392	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72890398	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72892604	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72892631	0.81[EUR][1000 genomes]
rs72892638	0.86[EUR][1000 genomes]
rs72892656	0.86[EUR][1000 genomes]
rs72892689	0.86[EUR][1000 genomes]
rs72892694	0.86[EUR][1000 genomes]
rs72892702	0.86[EUR][1000 genomes]
rs72894503	0.86[EUR][1000 genomes]
rs72894513	0.86[EUR][1000 genomes]
rs72894523	0.86[EUR][1000 genomes]
rs72894527	0.86[EUR][1000 genomes]
rs72894533	0.86[EUR][1000 genomes]
rs72894535	0.86[EUR][1000 genomes]
rs72894537	0.86[EUR][1000 genomes]
rs72894539	0.86[EUR][1000 genomes]
rs72894544	0.86[EUR][1000 genomes]
rs72894546	0.86[EUR][1000 genomes]
rs72894570	0.86[EUR][1000 genomes]
rs72894585	0.86[EUR][1000 genomes]
rs72894593	0.86[EUR][1000 genomes]
rs72894596	0.86[EUR][1000 genomes]
rs72896508	0.86[EUR][1000 genomes]
rs72896517	0.86[EUR][1000 genomes]
rs72896518	0.86[EUR][1000 genomes]
rs72896520	0.86[EUR][1000 genomes]
rs72896524	0.86[EUR][1000 genomes]
rs72896528	0.86[EUR][1000 genomes]
rs72896534	0.86[EUR][1000 genomes]
rs72896555	0.86[EUR][1000 genomes]
rs72896556	0.86[EUR][1000 genomes]
rs72896558	0.86[EUR][1000 genomes]
rs72896559	0.86[EUR][1000 genomes]
rs72896560	0.86[EUR][1000 genomes]
rs72896567	0.86[EUR][1000 genomes]
rs72896581	0.86[EUR][1000 genomes]
rs72896586	0.83[EUR][1000 genomes]
rs72896598	0.86[EUR][1000 genomes]
rs72898507	0.86[EUR][1000 genomes]
rs72898512	0.86[EUR][1000 genomes]
rs72898513	0.86[EUR][1000 genomes]
rs72898514	0.86[EUR][1000 genomes]
rs72898516	0.86[EUR][1000 genomes]
rs72898517	0.86[EUR][1000 genomes]
rs72898522	0.86[EUR][1000 genomes]
rs72898525	0.86[EUR][1000 genomes]
rs72898529	0.86[EUR][1000 genomes]
rs72898532	0.86[EUR][1000 genomes]
rs72898535	0.86[EUR][1000 genomes]
rs72898538	0.83[EUR][1000 genomes]
rs72898539	0.86[EUR][1000 genomes]
rs72898542	0.86[EUR][1000 genomes]
rs72898545	0.83[EUR][1000 genomes]
rs72898548	0.86[EUR][1000 genomes]
rs72898555	0.86[EUR][1000 genomes]
rs72898558	0.86[EUR][1000 genomes]
rs72898562	0.83[EUR][1000 genomes]
rs72898566	0.86[EUR][1000 genomes]
rs72898569	0.86[EUR][1000 genomes]
rs72898573	0.86[EUR][1000 genomes]
rs72898574	0.86[EUR][1000 genomes]
rs72898578	0.83[EUR][1000 genomes]
rs72898581	0.86[EUR][1000 genomes]
rs72900766	0.87[AMR][1000 genomes]
rs72900772	0.87[AMR][1000 genomes]
rs72900775	0.87[AMR][1000 genomes]
rs72900780	0.87[AMR][1000 genomes]
rs7562034	0.86[EUR][1000 genomes]
rs7565260	0.86[EUR][1000 genomes]
rs7566497	0.87[AMR][1000 genomes]
rs7567370	0.86[EUR][1000 genomes]
rs7577407	0.86[EUR][1000 genomes]
rs7597417	0.86[EUR][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	nsv1009882	chr2:183213152-184171519	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1005281	chr2:183803173-184093877	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv875485	chr2:183827018-184195265	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1010799	chr2:183855680-184244721	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv536072	chr2:183855680-184244721	Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv1003519	chr2:183885544-184015868	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:183846000-183902000	Weak transcription	Lung	lung
2	chr2:183878800-183902000	Weak transcription	Esophagus	oesophagus
3	chr2:183889800-183902000	Weak transcription	Gastric	stomach
4	chr2:183891400-183901800	Weak transcription	Small Intestine	intestine
5	chr2:183894600-183902000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:183894600-183902000	Weak transcription	Pancreas	Pancrea
7	chr2:183897800-183901800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:183899600-183901600	Flanking Active TSS	Osteobl	bone
9	chr2:183899600-183903800	Active TSS	Brain Angular Gyrus	brain
10	chr2:183899600-183904200	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr2:183899800-183901800	Flanking Active TSS	HUVEC	blood vessel
12	chr2:183899800-183903400	Active TSS	H1 Cell Line	embryonic stem cell
13	chr2:183899800-183903600	Active TSS	K562	blood
14	chr2:183899800-183903800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:183899800-183904000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr2:183900000-183901600	Flanking Active TSS	Colon Smooth Muscle	Colon
17	chr2:183900000-183901800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr2:183900000-183902200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr2:183900000-183903600	Active TSS	HMEC	breast
20	chr2:183900200-183901600	Enhancers	Brain Substantia Nigra	brain
21	chr2:183900200-183901800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr2:183900200-183902200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:183900200-183902400	Active TSS	Fetal Brain Male	brain
24	chr2:183900200-183902400	Active TSS	Right Atrium	heart
25	chr2:183900200-183903600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:183900200-183903600	Active TSS	Hela-S3	cervix
27	chr2:183900200-183903600	Active TSS	NHLF	lung
28	chr2:183900200-183903800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr2:183900200-183904000	Active TSS	Aorta	Aorta
30	chr2:183900200-183904000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr2:183900200-183904000	Active TSS	Psoas Muscle	Psoas
32	chr2:183900400-183901600	Weak transcription	Stomach Mucosa	stomach
33	chr2:183900400-183901600	Enhancers	GM12878-XiMat	blood
34	chr2:183900400-183901800	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr2:183900400-183901800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr2:183900400-183901800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr2:183900400-183902000	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr2:183900400-183902000	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr2:183900400-183902400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr2:183900400-183902400	Enhancers	Dnd41	blood
41	chr2:183900400-183903400	Active TSS	Skeletal Muscle Female	skeletal muscle
42	chr2:183900400-183903800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr2:183900400-183904000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr2:183900400-183904000	Active TSS	Right Ventricle	heart
45	chr2:183900600-183901600	Enhancers	Primary B cells from cord blood	blood
46	chr2:183900600-183902000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr2:183900600-183902000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr2:183900600-183902400	Flanking Active TSS	Adipose Nuclei	Adipose
49	chr2:183900600-183903400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr2:183900600-183903600	Active TSS	HUES48 Cell Line	embryonic stem cell

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