Variant report

Variant	rs2080227
Chromosome Location	chr2:63081759-63081760
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10153716	0.88[ASN][1000 genomes]
rs1022110	0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs11682530	0.92[YRI][hapmap];0.91[AFR][1000 genomes]
rs11688816	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs11893131	0.85[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12328837	0.81[YRI][hapmap]
rs12713468	0.80[CEU][hapmap];0.84[AFR][1000 genomes]
rs12989754	0.88[YRI][hapmap]
rs12994674	0.81[AFR][1000 genomes]
rs13013218	0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs13398408	0.92[YRI][hapmap]
rs13410889	0.83[CHB][hapmap];0.83[ASN][1000 genomes]
rs13418889	0.94[AFR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1468748	0.80[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.85[ASN][1000 genomes]
rs1553832	0.81[CEU][hapmap]
rs17027429	0.80[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1828398	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1877026	0.83[CHB][hapmap]
rs189671	0.81[CEU][hapmap]
rs2058567	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2075375	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs2136737	0.81[CEU][hapmap]
rs2215870	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs2421816	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2430388	0.84[CEU][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs2539978	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2539980	0.80[CEU][hapmap]
rs2539981	0.91[AFR][1000 genomes]
rs2539982	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2539984	0.92[ASN][1000 genomes]
rs2539987	0.84[CEU][hapmap]
rs2710637	0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs2710638	0.83[YRI][hapmap]
rs2710639	0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2710640	0.80[AFR][1000 genomes]
rs34104251	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs360797	1.00[YRI][hapmap]
rs360799	0.92[YRI][hapmap];0.84[AFR][1000 genomes]
rs360807	1.00[YRI][hapmap]
rs4461246	0.84[CEU][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs4671050	0.96[YRI][hapmap]
rs4671051	0.90[ASN][1000 genomes]
rs6545969	0.83[YRI][hapmap]
rs6545971	0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6545972	0.80[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6545973	0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6705798	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6714241	0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs6757128	0.83[YRI][hapmap]
rs7557501	0.80[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7562149	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.88[ASN][1000 genomes]
rs7567923	0.80[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7571916	0.94[ASN][1000 genomes]
rs7573756	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs7591708	0.82[CHB][hapmap]
rs9678329	0.82[AFR][1000 genomes]
rs9789661	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs9973612	0.95[JPT][hapmap];0.88[YRI][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	nsv535767	chr2:62461582-63413596	Bivalent Enhancer Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv3417336	chr2:62957866-63749654	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv428041	chr2:63027947-63206574	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1006848	chr2:63061816-63631407	Weak transcription Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63020600-63082000	Weak transcription	Pancreas	Pancrea
2	chr2:63031000-63083000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:63031400-63082000	Weak transcription	Thymus	Thymus
4	chr2:63040600-63082000	Weak transcription	Lung	lung
5	chr2:63046400-63101800	Weak transcription	Brain Angular Gyrus	brain
6	chr2:63050600-63091800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr2:63052000-63099600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr2:63052200-63098200	Weak transcription	Hela-S3	cervix
9	chr2:63054600-63099800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr2:63054800-63091600	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr2:63055000-63082000	Weak transcription	Esophagus	oesophagus
12	chr2:63056400-63081800	Weak transcription	NHLF	lung
13	chr2:63060800-63081800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:63061200-63115200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr2:63061400-63102000	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr2:63061600-63082000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr2:63062000-63082400	Weak transcription	HMEC	breast
18	chr2:63062000-63093000	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr2:63063000-63081800	Weak transcription	Fetal Stomach	stomach
20	chr2:63071200-63097200	Strong transcription	HepG2	liver
21	chr2:63072000-63086200	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr2:63072200-63082800	Weak transcription	Primary T cells from cord blood	blood
23	chr2:63072200-63083400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr2:63072600-63101800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr2:63072800-63083600	Weak transcription	Right Ventricle	heart
26	chr2:63073400-63083800	Weak transcription	Fetal Heart	heart
27	chr2:63073400-63093000	Weak transcription	Primary B cells from cord blood	blood
28	chr2:63073600-63083200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr2:63073800-63082000	Weak transcription	Fetal Lung	lung
30	chr2:63073800-63082800	Weak transcription	NHEK	skin
31	chr2:63073800-63091800	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr2:63073800-63094600	Weak transcription	GM12878-XiMat	blood
33	chr2:63074600-63084200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr2:63074800-63091400	Weak transcription	Colon Smooth Muscle	Colon
35	chr2:63074800-63101600	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr2:63075200-63082000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr2:63075400-63089400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr2:63075600-63093200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:63075800-63083400	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr2:63076400-63101800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr2:63076600-63082000	Weak transcription	Fetal Intestine Large	intestine
42	chr2:63076600-63082800	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr2:63076600-63083600	Weak transcription	Fetal Kidney	kidney
44	chr2:63078400-63084200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr2:63078600-63083600	Strong transcription	A549	lung
46	chr2:63078800-63082800	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr2:63079000-63083000	Weak transcription	Gastric	stomach
48	chr2:63079000-63092000	Weak transcription	Primary B cells from peripheral blood	blood
49	chr2:63079000-63101800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr2:63079400-63102000	Weak transcription	HSMMtube	muscle

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