Variant report

Variant	rs2971875
Chromosome Location	chr2:54901134-54901135
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54898899..54901777-chr2:54904985..54907433,2	K562	blood:
2	chr2:54899732..54901951-chr2:54909870..54911861,2	MCF-7	breast:
3	chr2:54891342..54894033-chr2:54900112..54903106,2	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10165490	0.80[CEU][hapmap]
rs1047499	0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12467581	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12624153	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs1510611	0.86[JPT][hapmap]
rs1541854	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs168503	0.85[EUR][1000 genomes]
rs168506	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs168508	0.81[EUR][1000 genomes]
rs171350	0.82[EUR][1000 genomes]
rs17416806	0.81[EUR][1000 genomes]
rs1821138	0.82[EUR][1000 genomes]
rs187124	0.87[EUR][1000 genomes]
rs191628	0.87[EUR][1000 genomes]
rs2048371	0.82[ASN][1000 genomes]
rs2271322	0.83[ASN][1000 genomes]
rs2292356	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2292357	0.85[ASN][1000 genomes]
rs2567835	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2931463	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2931464	0.81[EUR][1000 genomes]
rs2941586	0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2941587	0.83[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2941591	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2941595	0.82[EUR][1000 genomes]
rs2971877	0.82[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2971879	0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2971883	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2971887	0.82[EUR][1000 genomes]
rs2971889	0.84[EUR][1000 genomes]
rs354209	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs354213	0.80[EUR][1000 genomes]
rs354214	0.89[EUR][1000 genomes]
rs354226	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs354228	0.83[EUR][1000 genomes]
rs354231	0.95[CHB][hapmap];0.85[EUR][1000 genomes]
rs354236	0.92[CEU][hapmap];0.82[CHB][hapmap];0.81[EUR][1000 genomes]
rs354237	0.88[CEU][hapmap];0.82[CHB][hapmap]
rs354238	0.88[CEU][hapmap];0.82[CHB][hapmap]
rs3796014	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4444573	0.81[EUR][1000 genomes]
rs4455199	0.80[EUR][1000 genomes]
rs4519562	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4671960	0.91[CEU][hapmap];0.82[CHB][hapmap];0.80[JPT][hapmap];0.82[EUR][1000 genomes]
rs4671961	0.92[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes]
rs6545434	0.81[EUR][1000 genomes]
rs6706372	0.83[CHB][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6731661	0.81[EUR][1000 genomes]
rs6732949	0.81[EUR][1000 genomes]
rs6734658	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6748816	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6760298	0.86[JPT][hapmap]
rs7607451	0.83[CHB][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs907135	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv582024	chr2:54894649-54999712	Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54894600-54902200	Weak transcription	Psoas Muscle	Psoas
2	chr2:54895800-54902200	Weak transcription	Ovary	ovary
3	chr2:54896800-54902400	Weak transcription	K562	blood
4	chr2:54897000-54903800	Weak transcription	Brain Germinal Matrix	brain
5	chr2:54897200-54907800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr2:54897600-54902800	Weak transcription	Gastric	stomach
7	chr2:54897800-54901200	Strong transcription	A549	lung
8	chr2:54898000-54901400	Weak transcription	Dnd41	blood
9	chr2:54898200-54902600	Weak transcription	Fetal Heart	heart
10	chr2:54898200-54907000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr2:54898400-54902800	Weak transcription	Aorta	Aorta
12	chr2:54898400-54904600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:54898600-54901200	Weak transcription	Fetal Brain Male	brain
14	chr2:54898600-54901400	Enhancers	HepG2	liver
15	chr2:54898600-54901600	Weak transcription	Brain Substantia Nigra	brain
16	chr2:54898600-54903400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:54898600-54907800	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr2:54898800-54901200	Enhancers	Liver	Liver
19	chr2:54899200-54901200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr2:54899200-54901400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:54899200-54903400	Enhancers	Pancreas	Pancrea
22	chr2:54899200-54903400	Enhancers	Spleen	Spleen
23	chr2:54899400-54901800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr2:54899400-54902000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr2:54899400-54902000	Enhancers	Colon Smooth Muscle	Colon
26	chr2:54899600-54901200	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr2:54899600-54901200	Enhancers	Primary B cells from peripheral blood	blood
28	chr2:54899600-54902600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr2:54899600-54903000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:54899600-54903200	Weak transcription	NH-A	brain
31	chr2:54899800-54901200	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr2:54899800-54901400	Enhancers	Primary B cells from cord blood	blood
33	chr2:54899800-54901400	Enhancers	Right Atrium	heart
34	chr2:54899800-54901600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr2:54899800-54902000	Enhancers	Left Ventricle	heart
36	chr2:54899800-54902800	Enhancers	Fetal Lung	lung
37	chr2:54899800-54903000	Weak transcription	HSMM	muscle
38	chr2:54900000-54901200	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr2:54900000-54901400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr2:54900000-54902600	Enhancers	Fetal Thymus	thymus
41	chr2:54900000-54908600	Enhancers	NHDF-Ad	bronchial
42	chr2:54900200-54901200	Enhancers	Primary T cells from cord blood	blood
43	chr2:54900200-54901200	Enhancers	Primary hematopoietic stem cells	blood
44	chr2:54900200-54901200	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr2:54900200-54901200	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr2:54900200-54901200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr2:54900200-54901200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr2:54900200-54901200	Genic enhancers	HSMMtube	muscle
49	chr2:54900200-54901400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr2:54900200-54901400	Enhancers	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links