Variant report

Variant	rs12029889
Chromosome Location	chr1:91997333-91997334
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:91965969..91969419-chr1:91995771..91997473,3	K562	blood:
2	chr1:91966567..91968873-chr1:91994859..91997447,3	K562	blood:

Variant related genes	Relation type
ENSG00000097046	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10399689	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10399810	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10399813	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10399814	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10493849	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10493850	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10493851	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10782953	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10874758	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10874782	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11164877	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11164899	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11164913	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11164915	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12024529	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12025632	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12027099	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12028436	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12031239	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12035234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12035345	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12036176	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12036298	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12046667	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12057283	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12070660	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12758662	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12759236	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12759724	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13447523	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1508588	0.86[EUR][1000 genomes]
rs1531232	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1876264	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2219394	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2297709	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2893175	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35504045	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4658225	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs745732	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12029889	CDC7	cis	brain	BrainEAC
rs12029889	CDC7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:91967800-92009600	Weak transcription	Thymus	Thymus
2	chr1:91983000-92002600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr1:91984400-91998000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:91984600-91997800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr1:91985000-92000400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:91989200-91997800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr1:91989400-92002800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:91990000-91999400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr1:91990800-91998000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:91990800-91998000	Weak transcription	Fetal Heart	heart
11	chr1:91990800-92000800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr1:91991200-91997800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:91993200-91997800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr1:91994600-92002200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:91994800-91997800	Weak transcription	Fetal Kidney	kidney
16	chr1:91995400-92002200	Weak transcription	NHDF-Ad	bronchial
17	chr1:91995400-92002400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:91995800-92001200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr1:91995800-92003000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr1:91996000-91998000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr1:91996000-92002800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr1:91996200-91997800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr1:91996200-91997800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr1:91996200-91998000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr1:91996200-91998200	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr1:91996400-91997800	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr1:91996400-91998000	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr1:91996400-91998400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr1:91997200-91998200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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