Variant report

Variant	rs12070660
Chromosome Location	chr1:91991446-91991447
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:91965752..91967867-chr1:91990688..91992690,2	K562	blood:
2	chr1:91978959..91981332-chr1:91989401..91992669,3	K562	blood:
3	chr1:91988742..91991718-chr1:92001442..92003579,3	K562	blood:
4	chr1:91990049..91992908-chr1:91998911..92000736,2	K562	blood:

Variant related genes	Relation type
ENSG00000097046	Chromatin interaction

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

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

rs_ID	r²[population]
rs10399689	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10399810	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10399813	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10399814	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10493849	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10493850	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10493851	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10782953	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10874758	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10874782	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11164877	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11164899	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11164913	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11164915	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12024529	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12025632	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12027099	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12028436	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12029889	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12031239	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12035234	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12035345	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12036176	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12036298	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12046667	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12057283	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12758662	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12759236	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12759724	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13447523	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1508588	0.90[EUR][1000 genomes]
rs1531232	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1876264	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2219394	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2297709	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2893175	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35504045	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4658225	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs745732	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[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
rs12070660	CDC7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:91967800-92009600	Weak transcription	Thymus	Thymus
2	chr1:91968000-91991600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:91968400-91992000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr1:91972400-91992400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr1:91974400-91992000	Weak transcription	HUVEC	blood vessel
6	chr1:91975000-91995200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:91975600-91991600	Weak transcription	NHLF	lung
8	chr1:91977600-91992600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:91977800-91995200	Weak transcription	HMEC	breast
10	chr1:91978800-91993400	Weak transcription	Osteobl	bone
11	chr1:91980000-91991600	Weak transcription	Placenta	Placenta
12	chr1:91980200-91992000	Weak transcription	Fetal Kidney	kidney
13	chr1:91980400-91991600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:91980600-91992400	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr1:91980600-91995800	Weak transcription	HSMM	muscle
16	chr1:91981000-91991600	Weak transcription	Brain Germinal Matrix	brain
17	chr1:91981000-91995200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:91983000-92002600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr1:91983200-91995400	Weak transcription	Hela-S3	cervix
20	chr1:91983200-91995400	Weak transcription	NHEK	skin
21	chr1:91983400-91995000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr1:91983400-91995200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:91984000-91991600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:91984400-91992200	Weak transcription	Fetal Thymus	thymus
25	chr1:91984400-91994000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr1:91984400-91998000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:91984600-91994400	Weak transcription	Fetal Muscle Leg	muscle
28	chr1:91984600-91995200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:91984600-91997800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr1:91985000-92000400	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr1:91987200-91993400	Weak transcription	Colon Smooth Muscle	Colon
32	chr1:91988600-91993200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr1:91989200-91997800	Weak transcription	Primary hematopoietic stem cells	blood
34	chr1:91989400-91997200	Weak transcription	GM12878-XiMat	blood
35	chr1:91989400-92002800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr1:91989800-91995400	Weak transcription	A549	lung
37	chr1:91990000-91999400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr1:91990800-91992400	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr1:91990800-91992400	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr1:91990800-91993600	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr1:91990800-91995400	Enhancers	NHDF-Ad	bronchial
42	chr1:91990800-91998000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr1:91990800-91998000	Weak transcription	Fetal Heart	heart
44	chr1:91990800-92000800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr1:91991000-91992600	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr1:91991000-91994600	Enhancers	Fetal Stomach	stomach
47	chr1:91991000-91995200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr1:91991000-91996400	Weak transcription	Dnd41	blood
49	chr1:91991200-91994800	Weak transcription	K562	blood
50	chr1:91991200-91997800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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