Variant report

Variant	rs3845627
Chromosome Location	chr1:160489974-160489975
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10797069	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10797072	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10797076	0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10797077	0.88[CHB][hapmap];0.92[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs10797078	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10908782	0.81[AMR][1000 genomes]
rs10908787	0.86[TSI][hapmap];0.83[AMR][1000 genomes]
rs10908788	0.86[TSI][hapmap];0.83[AMR][1000 genomes]
rs10908790	0.81[AMR][1000 genomes]
rs11265418	0.84[AMR][1000 genomes]
rs11265432	0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11265433	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11265436	1.00[CEU][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11265438	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1149381	0.83[EUR][1000 genomes]
rs12128290	0.84[AMR][1000 genomes]
rs1324734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1408597	0.95[TSI][hapmap]
rs1466933	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1503856	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1503859	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1503860	0.88[CHB][hapmap];0.85[JPT][hapmap]
rs1553458	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1590450	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2050523	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2134705	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2369721	0.83[AMR][1000 genomes]
rs2369723	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2438181	0.81[EUR][1000 genomes]
rs349250	0.83[EUR][1000 genomes]
rs349251	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs3737788	0.81[ASN][1000 genomes]
rs3737789	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3766390	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3898642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3903887	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3903888	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3904694	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4145896	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4268352	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6413899	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6427521	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6427523	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6427525	0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6427528	0.88[CHB][hapmap];0.85[JPT][hapmap]
rs6427530	0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6659814	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6662885	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6668881	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6680709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6680920	0.83[EUR][1000 genomes]
rs6689237	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6691593	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6696595	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6700440	0.86[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6700764	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs724985	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7413789	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7519809	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7519913	0.81[EUR][1000 genomes]
rs7533828	0.81[AMR][1000 genomes]
rs7535796	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7543788	1.00[CEU][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7547372	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7555581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]

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	esv1829614	chr1:160465291-160595000	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv872491	chr1:160470258-160580549	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160486000-160490000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:160488000-160490800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
3	chr1:160488600-160493000	Enhancers	Primary hematopoietic stem cells	blood
4	chr1:160488800-160491000	Enhancers	Dnd41	blood
5	chr1:160488800-160492000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
6	chr1:160489000-160491000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:160489000-160491800	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr1:160489000-160491800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
9	chr1:160489000-160492400	Flanking Active TSS	Primary T cells from cord blood	blood
10	chr1:160489000-160492600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
11	chr1:160489200-160490000	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr1:160489200-160490000	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr1:160489200-160490000	Enhancers	Fetal Thymus	thymus
14	chr1:160489200-160490200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:160489200-160490600	Enhancers	Thymus	Thymus
16	chr1:160489200-160490800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:160489200-160490800	Enhancers	Fetal Intestine Small	intestine
18	chr1:160489200-160491000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:160489200-160491200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
20	chr1:160489200-160491800	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr1:160489200-160492800	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr1:160489200-160493400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
23	chr1:160489400-160490200	Enhancers	H9 Cell Line	embryonic stem cell
24	chr1:160489400-160490800	Enhancers	Fetal Intestine Large	intestine
25	chr1:160489400-160491600	Flanking Active TSS	Primary B cells from peripheral blood	blood
26	chr1:160489400-160493200	Flanking Active TSS	Primary B cells from cord blood	blood
27	chr1:160489600-160490200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:160489600-160490400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr1:160489600-160490800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:160489600-160491200	Active TSS	Primary T killer memory cells from peripheral blood	blood
31	chr1:160489800-160490000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
32	chr1:160489800-160490000	Enhancers	Gastric	stomach
33	chr1:160489800-160490000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
34	chr1:160489800-160490200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr1:160489800-160490200	Enhancers	H1 Cell Line	embryonic stem cell
36	chr1:160489800-160490200	Flanking Active TSS	Duodenum Mucosa	Duodenum
37	chr1:160489800-160490200	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr1:160489800-160490200	Flanking Active TSS	NHEK	skin
39	chr1:160489800-160490400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr1:160489800-160490400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
41	chr1:160489800-160490400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
42	chr1:160489800-160490400	Flanking Active TSS	A549	lung
43	chr1:160489800-160490600	Flanking Active TSS	GM12878-XiMat	blood
44	chr1:160489800-160490800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
45	chr1:160489800-160490800	Enhancers	HMEC	breast
46	chr1:160489800-160491000	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr1:160489800-160491600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr1:160489800-160492600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
49	chr1:160489800-160492600	Enhancers	K562	blood

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