Variant report

Variant	rs2253760
Chromosome Location	chr2:54033988-54033989
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10183655	0.81[CEU][hapmap];0.87[CHB][hapmap];0.80[JPT][hapmap]
rs17039525	0.87[ASN][1000 genomes]
rs17045199	0.95[CHB][hapmap];0.87[ASN][1000 genomes]
rs17045452	0.82[CHB][hapmap]
rs2542571	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2542575	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2542577	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2542588	0.86[YRI][hapmap];0.89[AFR][1000 genomes]
rs2692514	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2692516	0.95[CHB][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2692534	0.95[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs2909261	0.93[ASN][1000 genomes]
rs2909459	0.82[CHB][hapmap]
rs3095756	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35487539	0.88[ASN][1000 genomes]
rs3731967	0.81[CEU][hapmap];0.87[CHB][hapmap]
rs3731970	0.81[ASN][1000 genomes]
rs3770407	0.81[ASN][1000 genomes]
rs3770408	0.81[ASN][1000 genomes]
rs58359565	0.89[ASN][1000 genomes]
rs62137566	0.82[ASN][1000 genomes]
rs6746965	0.82[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap]
rs698853	0.94[ASN][1000 genomes]
rs698855	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs7583622	0.86[CHB][hapmap];0.80[JPT][hapmap];0.88[ASN][1000 genomes]
rs766075	0.87[CHB][hapmap]
rs805310	0.83[CHB][hapmap]
rs805321	0.91[CHB][hapmap]
rs805328	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs805351	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs805352	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs805365	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs805386	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs805399	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs805401	0.91[CHB][hapmap]
rs805404	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs805408	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs805416	0.87[EUR][1000 genomes]
rs805426	0.91[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003263	chr2:53863287-54055359	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv535720	chr2:53863287-54055359	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv834058	chr2:53900674-54072011	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1009829	chr2:53980562-54051927	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS 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	13 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	chr2:54015200-54038200	Weak transcription	Small Intestine	intestine
2	chr2:54015200-54046200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr2:54015200-54046200	Weak transcription	Aorta	Aorta
4	chr2:54015200-54051600	Weak transcription	Stomach Mucosa	stomach
5	chr2:54015200-54053800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:54015600-54035600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr2:54015600-54035800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr2:54015600-54054600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr2:54015800-54038400	Weak transcription	Fetal Heart	heart
10	chr2:54015800-54054000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:54016400-54043000	Weak transcription	Gastric	stomach
12	chr2:54020200-54046200	Weak transcription	Colonic Mucosa	Colon
13	chr2:54020600-54047200	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr2:54020600-54048400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:54020600-54048600	Strong transcription	Osteobl	bone
16	chr2:54021000-54047200	Strong transcription	Primary B cells from peripheral blood	blood
17	chr2:54021000-54047200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr2:54021000-54047400	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr2:54021000-54048000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr2:54021200-54047200	Strong transcription	Placenta	Placenta
21	chr2:54021200-54047600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:54021400-54047000	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr2:54021400-54047000	Strong transcription	Fetal Thymus	thymus
24	chr2:54021600-54035000	Strong transcription	Liver	Liver
25	chr2:54021600-54046400	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr2:54021800-54047600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr2:54022000-54039400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr2:54022000-54044800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr2:54022000-54047000	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr2:54022000-54047000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr2:54022000-54047200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr2:54022000-54047600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr2:54022200-54039000	Strong transcription	Fetal Intestine Large	intestine
34	chr2:54022200-54046200	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr2:54022200-54046600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr2:54022200-54047200	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr2:54023000-54053800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr2:54024200-54043400	Strong transcription	Dnd41	blood
39	chr2:54024400-54035000	Weak transcription	HSMMtube	muscle
40	chr2:54024800-54039600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr2:54024800-54045400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr2:54025000-54040000	Weak transcription	K562	blood
43	chr2:54025800-54035400	Weak transcription	Pancreas	Pancrea
44	chr2:54025800-54036600	Weak transcription	Spleen	Spleen
45	chr2:54025800-54062000	Weak transcription	Right Ventricle	heart
46	chr2:54025800-54085600	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr2:54026400-54034000	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr2:54026600-54035800	Weak transcription	Brain Anterior Caudate	brain
49	chr2:54026600-54038000	Weak transcription	Fetal Brain Male	brain
50	chr2:54027200-54046400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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