Variant report

Variant	rs11058062
Chromosome Location	chr12:122903468-122903469
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:122902497..122904051-chr12:122964826..122966588,2	MCF-7	breast:
2	chr12:122879571..122888507-chr12:122899670..122909196,27	K562	blood:
3	chr12:122819260..122821230-chr12:122903461..122905626,2	K562	blood:
4	chr12:122902575..122904900-chr12:122907634..122909136,2	MCF-7	breast:
5	chr12:122902285..122904972-chr12:122905751..122909798,4	K562	blood:
6	chr12:122902598..122904483-chr12:122905269..122908349,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000033030	Chromatin interaction
ENSG00000257097	Chromatin interaction
ENSG00000130779	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10846839	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10846854	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10846879	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10846896	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10847103	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs11057562	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11057787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11057801	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11057810	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11057832	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11057894	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11057934	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11058001	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11058009	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11058010	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11058043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11058064	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11058099	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11058136	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11058143	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11058144	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11058159	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11058186	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11058206	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11058232	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11058237	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11058480	0.91[CHB][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap]
rs12227778	1.00[ASW][hapmap]
rs12229152	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12229345	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12424715	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12427143	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12427421	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2173581	1.00[ASW][hapmap];0.88[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3817012	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4758661	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4758672	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4758694	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4758697	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56861120	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56863652	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58062133	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58766840	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58853108	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61954399	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61954405	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61954416	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61954418	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61954421	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61954422	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61954424	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61954425	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61954427	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61954441	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61954442	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61954447	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61954450	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8181750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs882969	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11058062	TMED2	cis	cerebellum	SCAN
rs11058062	CIT	cis	cerebellum	SCAN
rs11058062	DHX37	cis	parietal	SCAN
rs11058062	TMED2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122860600-122905000	Weak transcription	Brain Germinal Matrix	brain
2	chr12:122863800-122905000	Weak transcription	Dnd41	blood
3	chr12:122884600-122905200	Weak transcription	Colonic Mucosa	Colon
4	chr12:122885200-122904600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr12:122885200-122905200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr12:122885200-122905400	Weak transcription	Fetal Thymus	thymus
7	chr12:122885200-122905400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr12:122885200-122906000	Weak transcription	Ovary	ovary
9	chr12:122885400-122905000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr12:122885600-122905400	Weak transcription	NH-A	brain
11	chr12:122886200-122905400	Weak transcription	Right Ventricle	heart
12	chr12:122887200-122906200	Weak transcription	Lung	lung
13	chr12:122887600-122904800	Weak transcription	HMEC	breast
14	chr12:122888800-122905000	Weak transcription	Esophagus	oesophagus
15	chr12:122889000-122904600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr12:122889000-122905000	Weak transcription	Fetal Muscle Leg	muscle
17	chr12:122890000-122905000	Weak transcription	Primary T cells from cord blood	blood
18	chr12:122891000-122905200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr12:122892200-122904000	Weak transcription	HSMMtube	muscle
20	chr12:122892200-122904800	Weak transcription	Brain Angular Gyrus	brain
21	chr12:122892600-122905000	Weak transcription	Fetal Intestine Large	intestine
22	chr12:122895200-122905200	Weak transcription	Fetal Heart	heart
23	chr12:122896200-122904800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr12:122896200-122905000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr12:122896400-122905600	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr12:122897200-122905000	Weak transcription	Spleen	Spleen
27	chr12:122898000-122904800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr12:122898000-122905000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr12:122898000-122905400	Weak transcription	Fetal Kidney	kidney
30	chr12:122898200-122905000	Weak transcription	Brain Substantia Nigra	brain
31	chr12:122898200-122905000	Weak transcription	Stomach Mucosa	stomach
32	chr12:122898200-122905000	Weak transcription	NHDF-Ad	bronchial
33	chr12:122898200-122905200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr12:122898200-122905600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr12:122898400-122904800	Weak transcription	Duodenum Mucosa	Duodenum
36	chr12:122898600-122904400	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr12:122898600-122904600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr12:122898600-122904600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr12:122898600-122904800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr12:122898600-122904800	Weak transcription	Brain Hippocampus Middle	brain
41	chr12:122898600-122905000	Weak transcription	Adipose Nuclei	Adipose
42	chr12:122898600-122905000	Weak transcription	Brain Anterior Caudate	brain
43	chr12:122898600-122905000	Weak transcription	Fetal Brain Female	brain
44	chr12:122898600-122905400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr12:122898800-122904800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr12:122898800-122904800	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr12:122898800-122905000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr12:122898800-122905000	Weak transcription	Fetal Brain Male	brain
49	chr12:122898800-122905200	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr12:122899000-122903600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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