Variant report

Variant	rs11524523
Chromosome Location	chr12:9826746-9826747
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:9799292..9802850-chr12:9823422..9827161,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256594	Chromatin interaction
ENSG00000256442	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1008611	0.83[ASN][1000 genomes]
rs10743821	0.83[ASN][1000 genomes]
rs10743822	0.83[ASN][1000 genomes]
rs10844418	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10844429	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10844449	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10844457	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10844476	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052303	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11052304	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11052305	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052311	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052342	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052366	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052367	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052430	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052431	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052434	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052718	0.89[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs11052785	0.83[ASN][1000 genomes]
rs11519377	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12309762	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12320830	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12371982	1.00[AFR][1000 genomes]
rs12578698	0.83[ASN][1000 genomes]
rs12578928	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12582616	1.00[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12810851	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12812783	1.00[AFR][1000 genomes]
rs12815393	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12817365	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12823699	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12825507	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12828602	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12828773	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12831453	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1990533	0.83[ASN][1000 genomes]
rs2114872	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2114873	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2192433	0.83[ASN][1000 genomes]
rs2192434	0.83[ASN][1000 genomes]
rs2192435	0.83[ASN][1000 genomes]
rs2192439	0.89[ASN][1000 genomes]
rs2401396	0.83[ASN][1000 genomes]
rs34201389	0.87[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs34850016	0.89[AFR][1000 genomes]
rs35237063	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4763264	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4763835	0.83[ASN][1000 genomes]
rs61913428	0.87[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6488109	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488122	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7310897	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7954062	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7969074	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972035	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7979758	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9630264	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9630265	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9668568	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs982511	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427903	chr12:9371593-9830668	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
4	esv1821732	chr12:9560087-9830668	Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv1823760	chr12:9560087-9830668	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv428271	chr12:9560087-9830668	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11524523	LOC374443	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9802400-9849800	Weak transcription	Pancreas	Pancrea
2	chr12:9807600-9847200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr12:9815200-9828400	Weak transcription	Liver	Liver
4	chr12:9815200-9840600	Weak transcription	Fetal Brain Male	brain
5	chr12:9815200-9841600	Weak transcription	Fetal Kidney	kidney
6	chr12:9815600-9833800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr12:9816200-9832600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr12:9816200-9840600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr12:9817200-9837800	Weak transcription	Aorta	Aorta
10	chr12:9818000-9839200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr12:9818000-9839800	Weak transcription	Ovary	ovary
12	chr12:9818000-9840000	Weak transcription	Fetal Intestine Large	intestine
13	chr12:9818000-9849800	Weak transcription	Brain Germinal Matrix	brain
14	chr12:9818200-9828600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr12:9818200-9840000	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr12:9822400-9827200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
17	chr12:9823000-9829800	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
18	chr12:9824200-9827400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
19	chr12:9824200-9827800	Flanking Active TSS	Primary T cells from cord blood	blood
20	chr12:9824200-9828200	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
21	chr12:9824200-9828200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
22	chr12:9824400-9832600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr12:9824600-9827200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
24	chr12:9824600-9827200	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
25	chr12:9824800-9827200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
26	chr12:9825200-9827200	Enhancers	Placenta Amnion	Placenta Amnion
27	chr12:9825400-9827200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr12:9825400-9827200	Enhancers	Fetal Heart	heart
29	chr12:9825600-9826800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
30	chr12:9825600-9826800	Enhancers	Monocytes-CD14+_RO01746	blood
31	chr12:9825600-9827000	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr12:9825600-9827200	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr12:9825600-9827200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr12:9825600-9827200	Transcr. at gene 5' and 3'	Primary B cells from peripheral blood	blood
35	chr12:9825600-9827200	Enhancers	Primary hematopoietic stem cells	blood
36	chr12:9825600-9827200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr12:9825600-9827400	Enhancers	HMEC	breast
38	chr12:9825600-9827600	Flanking Active TSS	GM12878-XiMat	blood
39	chr12:9825800-9826800	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr12:9825800-9826800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr12:9825800-9826800	Enhancers	HSMMtube	muscle
42	chr12:9825800-9827000	Enhancers	Placenta	Placenta
43	chr12:9825800-9827000	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
44	chr12:9825800-9827000	Enhancers	Right Ventricle	heart
45	chr12:9825800-9827200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr12:9825800-9827200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr12:9825800-9827200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr12:9825800-9827200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr12:9825800-9827200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr12:9825800-9827200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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