Variant report

Variant	rs11046093
Chromosome Location	chr12:21661707-21661708
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:21654009..21656768-chr12:21660013..21662532,3	MCF-7	breast:
2	chr12:21659626..21662190-chr12:21669299..21671528,2	K562	blood:

Variant related genes	Relation type
ENSG00000004700	Chromatin interaction
ENSG00000111711	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1029931	0.81[CHD][hapmap]
rs10492117	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs10770819	0.94[CHD][hapmap];0.91[MEX][hapmap]
rs10841833	0.86[CHD][hapmap];0.90[JPT][hapmap]
rs10841835	0.94[JPT][hapmap]
rs10841836	0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs10841837	0.83[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10841839	0.80[CHB][hapmap];0.83[CHD][hapmap]
rs10841840	0.80[CHB][hapmap];0.83[CHD][hapmap]
rs11046089	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs11046094	0.91[YRI][hapmap]
rs11046095	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11046098	0.80[CHB][hapmap];0.92[CHD][hapmap]
rs12231436	0.86[CHD][hapmap];0.90[JPT][hapmap]
rs12423412	0.83[CHD][hapmap];0.90[JPT][hapmap]
rs12582513	0.88[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12582514	1.00[ASW][hapmap];0.92[CEU][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12822436	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12829302	0.90[JPT][hapmap]
rs12833589	0.90[JPT][hapmap]
rs2110159	0.81[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap]
rs2159944	0.81[CHD][hapmap]
rs2284393	0.89[CHD][hapmap];0.90[JPT][hapmap]
rs2284394	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs2300211	0.81[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap]
rs2417991	0.84[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs34965831	0.90[ASN][1000 genomes]
rs35538394	0.96[ASN][1000 genomes]
rs3782661	0.82[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs4762834	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs4762835	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs61926331	0.86[ASN][1000 genomes]
rs61926332	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898896	chr12:21561645-21695584	Strong transcription Bivalent Enhancer Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1043936	chr12:21562673-21979030	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv557741	chr12:21578559-22169854	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv1054220	chr12:21612158-21692103	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1036084	chr12:21631009-21792756	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs11046093	PYROXD1	cis	cerebellum	SCAN
rs11046093	LOC642732	Cis_1M	lymphoblastoid	RTeQTL
rs11046093	RECQL	cis	cerebellum	SCAN
rs11046093	PYROXD1	Cis_1M	lymphoblastoid	RTeQTL
rs11046093	PYROXD1	cis	parietal	SCAN
rs11046093	LOC642732///PYROXD1	Cis_1M	lymphoblastoid	RTeQTL
rs11046093	RECQL	cis	parietal	SCAN
rs11046093	LOC642732	trans	multi-tissue	Pritchard
rs11046093	RECQL	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21655400-21674800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:21655600-21661800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:21655600-21666000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr12:21656000-21671800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr12:21656000-21672800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr12:21656000-21674000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr12:21656000-21674600	Weak transcription	Fetal Kidney	kidney
8	chr12:21656200-21662000	Weak transcription	Fetal Intestine Small	intestine
9	chr12:21656200-21662000	Weak transcription	Fetal Stomach	stomach
10	chr12:21656200-21662200	Weak transcription	HSMM	muscle
11	chr12:21656200-21664000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr12:21656200-21665000	Weak transcription	HSMMtube	muscle
13	chr12:21656200-21665200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr12:21656200-21665600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr12:21656200-21666200	Weak transcription	Colonic Mucosa	Colon
16	chr12:21656200-21669800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr12:21656200-21671800	Weak transcription	Thymus	Thymus
18	chr12:21656200-21680000	Weak transcription	Right Ventricle	heart
19	chr12:21656400-21662600	Weak transcription	Brain Germinal Matrix	brain
20	chr12:21656400-21668000	Weak transcription	Fetal Lung	lung
21	chr12:21656400-21680200	Weak transcription	Aorta	Aorta
22	chr12:21656600-21663800	Weak transcription	NHLF	lung
23	chr12:21656600-21665200	Weak transcription	NHEK	skin
24	chr12:21656600-21665400	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr12:21656600-21665800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr12:21656600-21669200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr12:21656800-21665800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr12:21656800-21666000	Weak transcription	Colon Smooth Muscle	Colon
29	chr12:21656800-21666600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr12:21656800-21671400	Weak transcription	Fetal Heart	heart
31	chr12:21656800-21680000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr12:21657000-21662800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr12:21657400-21662600	Weak transcription	Fetal Muscle Leg	muscle
34	chr12:21657400-21662800	Weak transcription	K562	blood
35	chr12:21657400-21665800	Weak transcription	Brain Hippocampus Middle	brain
36	chr12:21657400-21669800	Weak transcription	Brain Substantia Nigra	brain
37	chr12:21657400-21680000	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr12:21657600-21663800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr12:21657600-21665600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr12:21657600-21665800	Weak transcription	Brain Cingulate Gyrus	brain
41	chr12:21657600-21665800	Weak transcription	Esophagus	oesophagus
42	chr12:21657600-21665800	Weak transcription	Lung	lung
43	chr12:21657600-21665800	Weak transcription	Ovary	ovary
44	chr12:21657600-21666400	Weak transcription	Psoas Muscle	Psoas
45	chr12:21657600-21666400	Weak transcription	Spleen	Spleen
46	chr12:21657600-21669600	Weak transcription	Brain Angular Gyrus	brain
47	chr12:21657600-21675000	Weak transcription	Small Intestine	intestine
48	chr12:21657600-21675400	Weak transcription	Fetal Brain Male	brain
49	chr12:21657600-21679800	Weak transcription	Pancreas	Pancrea
50	chr12:21657600-21680000	Weak transcription	Brain Inferior Temporal Lobe	brain

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