Variant report

Variant	rs7963590
Chromosome Location	chr12:56395689-56395690
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56395246..56396955-chr12:56435355..56437007,2	K562	blood:
2	chr12:56388289..56393996-chr12:56394860..56404076,14	K562	blood:
3	chr12:56395394..56397678-chr12:56412069..56414982,2	MCF-7	breast:
4	chr12:56395480..56397433-chr12:56414863..56417335,2	MCF-7	breast:
5	chr12:56391225..56393452-chr12:56393825..56395799,2	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RAB5B-2	chr12:56395523-56395732	NONHSAT028736
2	lnc-RAB5B-2	chr12:56395591-56395689	NONHSAT028733

No data

Variant related genes	Relation type
ENSG00000197728	Chromatin interaction
ENSG00000123411	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000139531	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs12099979	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12810011	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12815302	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12815387	0.89[EUR][1000 genomes]
rs12815488	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12818756	0.89[EUR][1000 genomes]
rs12831468	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1614219	0.87[EUR][1000 genomes]
rs1689511	0.84[EUR][1000 genomes]
rs1701706	0.87[EUR][1000 genomes]
rs17118262	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2131569	0.89[EUR][1000 genomes]
rs2456972	0.87[EUR][1000 genomes]
rs2658479	0.83[EUR][1000 genomes]
rs34228181	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs34303864	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs34406511	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs34485293	0.80[EUR][1000 genomes]
rs34507011	0.87[EUR][1000 genomes]
rs34602183	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs34650555	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs34921584	0.89[EUR][1000 genomes]
rs35485002	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs35666826	0.81[EUR][1000 genomes]
rs35961650	0.83[EUR][1000 genomes]
rs4759022	0.89[EUR][1000 genomes]
rs4759239	0.83[EUR][1000 genomes]
rs71459334	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs71459336	0.87[EUR][1000 genomes]
rs71459339	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs71459342	0.81[EUR][1000 genomes]
rs7298818	0.94[EUR][1000 genomes]
rs7300772	0.87[EUR][1000 genomes]
rs772922	0.87[EUR][1000 genomes]
rs772923	0.89[EUR][1000 genomes]
rs773115	0.91[EUR][1000 genomes]
rs7977537	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]

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	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv832424	chr12:56275226-56466917	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
3	nsv1043988	chr12:56348185-56534900	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv832427	chr12:56392545-56512774	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7963590	LOC644166///LOC644191///LOC728937///RPS26	Cis_1M	lymphoblastoid	RTeQTL
rs7963590	SUOX	cis	Thyroid	GTEx
rs7963590	PMEL	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56391600-56395800	Weak transcription	Aorta	Aorta
2	chr12:56391600-56397600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr12:56391600-56398600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr12:56391600-56399000	Weak transcription	Primary T cells from cord blood	blood
5	chr12:56391600-56400800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr12:56391800-56395800	Weak transcription	Esophagus	oesophagus
7	chr12:56391800-56396000	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr12:56391800-56396200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr12:56391800-56396200	Weak transcription	NHLF	lung
10	chr12:56391800-56396400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:56391800-56397000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr12:56391800-56397800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr12:56391800-56400600	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr12:56391800-56400600	Weak transcription	NHEK	skin
15	chr12:56392000-56395800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr12:56392000-56395800	Weak transcription	Colon Smooth Muscle	Colon
17	chr12:56392000-56395800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr12:56392000-56395800	Weak transcription	Osteobl	bone
19	chr12:56392000-56396000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr12:56392000-56396000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr12:56392000-56396000	Weak transcription	Brain Substantia Nigra	brain
22	chr12:56392000-56396000	Weak transcription	Fetal Lung	lung
23	chr12:56392000-56396200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr12:56392000-56396200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr12:56392000-56396200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr12:56392000-56396200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr12:56392000-56396200	Weak transcription	NH-A	brain
28	chr12:56392000-56396400	Weak transcription	Fetal Brain Female	brain
29	chr12:56392000-56396800	Weak transcription	Primary hematopoietic stem cells	blood
30	chr12:56392000-56397400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr12:56392000-56397400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr12:56392000-56397600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr12:56392000-56397600	Weak transcription	HSMM	muscle
34	chr12:56392000-56397800	Weak transcription	HSMMtube	muscle
35	chr12:56392000-56399200	Weak transcription	HUVEC	blood vessel
36	chr12:56392000-56400600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr12:56392000-56400600	Weak transcription	Fetal Thymus	thymus
38	chr12:56392000-56400600	Weak transcription	Right Atrium	heart
39	chr12:56392000-56400600	Weak transcription	HMEC	breast
40	chr12:56392000-56400800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr12:56392000-56400800	Weak transcription	GM12878-XiMat	blood
42	chr12:56392200-56395800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr12:56392200-56399800	Weak transcription	Hela-S3	cervix
44	chr12:56392400-56395800	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr12:56392400-56395800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr12:56392400-56395800	Weak transcription	Brain Hippocampus Middle	brain
47	chr12:56392400-56395800	Weak transcription	Lung	lung
48	chr12:56392400-56396000	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr12:56392400-56396000	Weak transcription	Placenta	Placenta
50	chr12:56392400-56396400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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