Variant report

Variant	rs11058562
Chromosome Location	chr12:123003317-123003318
allele	C/T
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	FOS	chr12:123003162-123003340	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr12:123003075-123003417	GM12891	blood:	n/a	n/a
3	POLR2A	chr12:123003170-123003798	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr12:123003204-123005678	K562	blood:	n/a	n/a
5	POLR2A	chr12:123003270-123005760	HepG2	liver:	n/a	n/a
6	STAT3	chr12:123003081-123003378	MCF10A-Er-Src	breast:	n/a	chr12:123003198-123003209 chr12:123003197-123003211
7	POLR2A	chr12:123003028-123003560	GM12892	blood:	n/a	n/a
8	POLR2A	chr12:123003300-123003475	MCF-7	breast:	n/a	n/a
9	POLR2A	chr12:123003054-123003595	SK-N-MC	brain:	n/a	n/a
10	STAT3	chr12:123003073-123003697	MCF10A-Er-Src	breast:	n/a	chr12:123003198-123003209 chr12:123003197-123003211
11	POLR2A	chr12:123003265-123003498	HepG2	liver:	n/a	n/a
12	FOS	chr12:123003121-123003361	MCF10A-Er-Src	breast:	n/a	n/a
13	FOS	chr12:123003096-123003372	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr12:123003092-123003710	GM12878	blood:	n/a	n/a
15	STAT3	chr12:123003062-123003388	MCF10A-Er-Src	breast:	n/a	chr12:123003198-123003209 chr12:123003197-123003211

Variant related genes	Relation type
RSRC2	TF binding region

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10161184	1.00[YRI][hapmap]
rs10744242	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.99[ASN][1000 genomes]
rs10773090	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs10773117	0.87[ASW][hapmap]
rs10773230	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.94[ASN][1000 genomes]
rs10846912	0.94[JPT][hapmap]
rs10846968	0.90[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap]
rs10846993	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs10847090	0.96[ASN][1000 genomes]
rs10847141	0.84[AMR][1000 genomes]
rs10847335	0.80[MKK][hapmap]
rs11058272	0.81[AFR][1000 genomes]
rs11058602	0.85[AMR][1000 genomes]
rs11059097	0.85[MEX][hapmap]
rs1129167	1.00[YRI][hapmap]
rs11610303	1.00[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11611668	0.84[CHD][hapmap];0.83[GIH][hapmap]
rs11614277	0.85[MEX][hapmap]
rs12370850	0.86[AMR][1000 genomes]
rs12371048	0.84[AFR][1000 genomes]
rs12812332	0.95[JPT][hapmap]
rs12817342	1.00[ASW][hapmap];0.85[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1532578	0.90[CHB][hapmap];0.83[JPT][hapmap];0.96[ASN][1000 genomes]
rs2133557	0.94[ASN][1000 genomes]
rs34864383	0.81[AMR][1000 genomes]
rs3825096	1.00[YRI][hapmap]
rs4356269	0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap]
rs4758657	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs4758658	1.00[ASW][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs4758660	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.94[ASN][1000 genomes]
rs4758692	0.90[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap]
rs4758695	0.86[GIH][hapmap]
rs57311174	0.99[ASN][1000 genomes]
rs58600355	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs61956119	0.94[ASN][1000 genomes]
rs61956121	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6416295	0.85[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap]
rs6488947	0.87[ASW][hapmap]
rs6489014	0.90[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap]
rs6489051	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.96[ASN][1000 genomes]
rs6489056	0.90[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.99[ASN][1000 genomes]
rs7134381	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.99[ASN][1000 genomes]
rs7136564	0.96[ASN][1000 genomes]
rs7296680	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs7297866	0.99[ASN][1000 genomes]
rs7298839	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7307867	0.99[ASN][1000 genomes]
rs7311573	0.90[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap]
rs7955513	0.90[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap]
rs7967928	0.92[ASN][1000 genomes]
rs9788228	0.81[CHD][hapmap]

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	nsv899570	chr12:122985057-123089209	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	93 gene(s)	inside rSNPs	diseases
2	nsv1041677	chr12:122991478-123114125	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	64 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11058562	RNF10	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122986200-123007600	Weak transcription	Right Atrium	heart
2	chr12:122986400-123007800	Strong transcription	Placenta	Placenta
3	chr12:122986800-123006600	Strong transcription	Brain Germinal Matrix	brain
4	chr12:122986800-123006800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:122986800-123007000	Strong transcription	Fetal Muscle Leg	muscle
6	chr12:122986800-123009400	Strong transcription	Fetal Muscle Trunk	muscle
7	chr12:122987000-123007800	Strong transcription	Fetal Thymus	thymus
8	chr12:122987400-123006800	Strong transcription	Duodenum Mucosa	Duodenum
9	chr12:122987400-123007000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr12:122987400-123007200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr12:122987400-123007400	Strong transcription	Thymus	Thymus
12	chr12:122987400-123007600	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr12:122987400-123007800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:122987400-123007800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr12:122987600-123003600	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr12:122987600-123004000	Strong transcription	Primary T helper cells PMA-I stimulated	--
17	chr12:122987600-123004600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr12:122987600-123006000	Strong transcription	Duodenum Smooth Muscle	Duodenum
19	chr12:122987600-123006400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr12:122987600-123006400	Strong transcription	Liver	Liver
21	chr12:122987600-123006400	Strong transcription	Brain Hippocampus Middle	brain
22	chr12:122987600-123006600	Strong transcription	Primary T cells from cord blood	blood
23	chr12:122987600-123006800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr12:122987600-123007000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr12:122987600-123007000	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr12:122987600-123007000	Strong transcription	Fetal Intestine Large	intestine
27	chr12:122987600-123007000	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr12:122987600-123007600	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr12:122987600-123007600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr12:122987600-123008000	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr12:122987800-123003400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr12:122987800-123003400	Strong transcription	Spleen	Spleen
33	chr12:122987800-123004000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr12:122987800-123004200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr12:122987800-123004600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
36	chr12:122987800-123004600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr12:122987800-123005600	Strong transcription	Pancreas	Pancrea
38	chr12:122987800-123005600	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr12:122987800-123006400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr12:122987800-123006400	Strong transcription	Primary hematopoietic stem cells	blood
41	chr12:122987800-123006400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr12:122987800-123006400	Strong transcription	Adipose Nuclei	Adipose
43	chr12:122987800-123006400	Strong transcription	Brain Inferior Temporal Lobe	brain
44	chr12:122987800-123006400	Strong transcription	Colon Smooth Muscle	Colon
45	chr12:122987800-123006400	Strong transcription	Rectal Smooth Muscle	rectum
46	chr12:122987800-123006400	Strong transcription	Skeletal Muscle Male	skeletal muscle
47	chr12:122987800-123006400	Strong transcription	Stomach Smooth Muscle	stomach
48	chr12:122987800-123006600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr12:122987800-123006600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr12:122987800-123006600	Strong transcription	Brain Anterior Caudate	brain

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