Variant report

Variant	rs4145153
Chromosome Location	chr12:62714343-62714344
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:62711848-62714783	K562	blood:	n/a	n/a
2	GATA1	chr12:62711592-62714373	PBDE	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:62653180..62655433-chr12:62713358..62715236,3	K562	blood:
2	chr12:62653169..62654680-chr12:62713358..62715291,2	K562	blood:

Variant related genes	Relation type
USP15	TF binding region
ENSG00000198673	Chromatin interaction
ENSG00000135655	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10747960	1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10877822	0.88[CEU][hapmap]
rs10877827	1.00[YRI][hapmap]
rs10877828	0.84[CEU][hapmap]
rs10877833	0.87[CEU][hapmap]
rs10877839	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11174442	0.88[CEU][hapmap]
rs11174451	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11174452	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11174455	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11174465	0.82[ASN][1000 genomes]
rs11514251	0.85[CEU][hapmap]
rs11836392	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12316469	0.88[CEU][hapmap]
rs12818222	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1390853	0.95[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs1390854	0.87[EUR][1000 genomes]
rs1532435	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17097891	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17120331	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1901240	1.00[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs57361004	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7305206	1.00[LWK][hapmap];1.00[MKK][hapmap]
rs767390	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7975633	0.88[CEU][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	nsv1035150	chr12:62615347-62785005	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1049465	chr12:62657011-62785005	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv1053403	chr12:62657011-62809413	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv530690	chr12:62678463-62999462	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4145153	SNORD59B	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:62684000-62716200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:62686200-62720200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:62686400-62736400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:62687200-62718200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:62687400-62720600	Weak transcription	Right Ventricle	heart
6	chr12:62689400-62716000	Weak transcription	Colonic Mucosa	Colon
7	chr12:62689600-62717400	Weak transcription	Brain Angular Gyrus	brain
8	chr12:62691200-62716400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr12:62691200-62736400	Weak transcription	Esophagus	oesophagus
10	chr12:62691200-62736600	Weak transcription	Lung	lung
11	chr12:62698400-62717600	Weak transcription	Brain Germinal Matrix	brain
12	chr12:62698400-62741800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr12:62698600-62715200	Weak transcription	Colon Smooth Muscle	Colon
14	chr12:62698600-62716400	Weak transcription	HepG2	liver
15	chr12:62698600-62720800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr12:62698600-62725800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr12:62698600-62745800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr12:62698800-62728600	Weak transcription	Fetal Heart	heart
19	chr12:62699800-62715200	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr12:62699800-62715400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr12:62699800-62736400	Weak transcription	Aorta	Aorta
22	chr12:62700000-62715200	Weak transcription	Brain Anterior Caudate	brain
23	chr12:62700000-62715400	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr12:62700000-62719000	Weak transcription	Fetal Brain Female	brain
25	chr12:62700000-62726600	Weak transcription	HSMMtube	muscle
26	chr12:62700000-62736400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr12:62700000-62736400	Weak transcription	Fetal Stomach	stomach
28	chr12:62700000-62737000	Weak transcription	NHLF	lung
29	chr12:62700000-62757000	Weak transcription	HUVEC	blood vessel
30	chr12:62700200-62715000	Weak transcription	NH-A	brain
31	chr12:62700200-62715400	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr12:62700200-62716000	Weak transcription	Osteobl	bone
33	chr12:62700200-62716400	Weak transcription	Brain Substantia Nigra	brain
34	chr12:62700200-62717800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr12:62700600-62716000	Weak transcription	HMEC	breast
36	chr12:62701600-62715200	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr12:62701600-62715800	Weak transcription	Thymus	Thymus
38	chr12:62701600-62717200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr12:62701600-62730800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr12:62701600-62738600	Weak transcription	Fetal Brain Male	brain
41	chr12:62701600-62742000	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr12:62701600-62769200	Weak transcription	NHEK	skin
43	chr12:62701800-62717200	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr12:62702000-62715400	Weak transcription	Placenta	Placenta
45	chr12:62702400-62715400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr12:62702400-62715400	Weak transcription	Duodenum Mucosa	Duodenum
47	chr12:62702400-62715400	Weak transcription	Fetal Kidney	kidney
48	chr12:62702400-62715800	Weak transcription	Stomach Smooth Muscle	stomach
49	chr12:62705800-62715400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr12:62706000-62715200	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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