Variant report

Variant	rs12025632
Chromosome Location	chr1:91986709-91986710
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:91984712..91986944-chr1:91994080..91996686,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10399689	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10399810	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10399813	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10399814	1.00[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10493849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10493850	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10493851	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10782953	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10874758	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10874782	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11164877	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164899	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11164913	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11164915	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12024529	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12027099	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12028436	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12029889	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12031239	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12035234	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12035345	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12036176	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12036298	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12046667	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12057283	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12070660	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12758662	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12759236	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12759724	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13447523	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1508588	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1531232	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1876264	1.00[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2219394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2297709	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2893175	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35504045	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4658225	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs745732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[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	nsv949516	chr1:91644418-92109261	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1009560	chr1:91897078-92270781	Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12025632	CDC7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:91967200-91989000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:91967400-91989000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:91967600-91990600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:91967800-92009600	Weak transcription	Thymus	Thymus
5	chr1:91968000-91991600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:91968200-91987400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:91968400-91992000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:91968600-91989000	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr1:91968600-91991000	Weak transcription	Fetal Stomach	stomach
10	chr1:91968800-91989000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr1:91968800-91991200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr1:91969200-91989000	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr1:91970800-91988800	Weak transcription	Fetal Brain Male	brain
14	chr1:91971000-91989000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr1:91971000-91991200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:91972400-91992400	Weak transcription	Fetal Muscle Trunk	muscle
17	chr1:91972800-91989000	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr1:91973000-91986800	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr1:91973400-91987000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:91974400-91992000	Weak transcription	HUVEC	blood vessel
21	chr1:91974800-91991000	Strong transcription	Dnd41	blood
22	chr1:91975000-91995200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr1:91975600-91991600	Weak transcription	NHLF	lung
24	chr1:91977600-91992600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:91977800-91995200	Weak transcription	HMEC	breast
26	chr1:91978800-91993400	Weak transcription	Osteobl	bone
27	chr1:91980000-91991600	Weak transcription	Placenta	Placenta
28	chr1:91980200-91992000	Weak transcription	Fetal Kidney	kidney
29	chr1:91980400-91991600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr1:91980600-91992400	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr1:91980600-91995800	Weak transcription	HSMM	muscle
32	chr1:91981000-91991600	Weak transcription	Brain Germinal Matrix	brain
33	chr1:91981000-91995200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:91982600-91988000	Weak transcription	Fetal Brain Female	brain
35	chr1:91983000-92002600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr1:91983200-91988400	Weak transcription	A549	lung
37	chr1:91983200-91988600	Weak transcription	Primary hematopoietic stem cells	blood
38	chr1:91983200-91989000	Weak transcription	Primary T cells from cord blood	blood
39	chr1:91983200-91989600	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr1:91983200-91995400	Weak transcription	Hela-S3	cervix
41	chr1:91983200-91995400	Weak transcription	NHEK	skin
42	chr1:91983400-91988000	Weak transcription	GM12878-XiMat	blood
43	chr1:91983400-91991400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr1:91983400-91995000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr1:91983400-91995200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr1:91983600-91988800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr1:91984000-91991600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr1:91984200-91991200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr1:91984400-91988600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr1:91984400-91992200	Weak transcription	Fetal Thymus	thymus

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