Variant report

Variant	rs1106766
Chromosome Location	chr12:57809456-57809457
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	chr12:57808026..57810781-chr12:57822669..57824932,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000179912	Chromatin interaction
ENSG00000258001	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11172134	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs11172147	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs11172181	0.91[AFR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11609805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11612551	0.83[MEX][hapmap]
rs11613352	1.00[CEU][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11614506	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12313306	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12315434	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2122982	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2229357	1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3741414	0.82[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4760254	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4760278	0.95[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4760355	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs540730	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56152729	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61352607	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73119306	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7397189	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7484541	0.81[ASN][1000 genomes]
rs7485577	0.83[MEX][hapmap]
rs7964492	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7971133	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7974833	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046013	chr12:57714676-57895167	Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv541502	chr12:57714676-57895167	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
3	nsv516655	chr12:57763520-57811414	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Urate levels	20884846	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1106766	IL23A	cis	parietal	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57753200-57823800	Weak transcription	Esophagus	oesophagus
2	chr12:57762800-57811800	Weak transcription	Pancreas	Pancrea
3	chr12:57766200-57816000	Weak transcription	Fetal Lung	lung
4	chr12:57770800-57824000	Weak transcription	Gastric	stomach
5	chr12:57774400-57819200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr12:57780800-57823200	Weak transcription	Spleen	Spleen
7	chr12:57783800-57823200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr12:57784200-57809800	Weak transcription	Osteobl	bone
9	chr12:57784200-57818000	Weak transcription	HSMM	muscle
10	chr12:57784400-57813600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr12:57784400-57816400	Weak transcription	NHLF	lung
12	chr12:57786400-57815600	Weak transcription	Fetal Brain Female	brain
13	chr12:57786600-57813400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr12:57787000-57811400	Weak transcription	Stomach Mucosa	stomach
15	chr12:57787800-57812000	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr12:57788600-57815200	Weak transcription	Fetal Intestine Large	intestine
17	chr12:57788600-57823200	Weak transcription	NHDF-Ad	bronchial
18	chr12:57789200-57823000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr12:57789400-57810400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr12:57789400-57813400	Weak transcription	Lung	lung
21	chr12:57789400-57823200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr12:57789600-57810200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr12:57789600-57811400	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr12:57789600-57815600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:57789600-57815800	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr12:57789600-57816200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr12:57789800-57809600	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr12:57789800-57813200	Weak transcription	Fetal Muscle Leg	muscle
29	chr12:57789800-57814400	Weak transcription	Duodenum Mucosa	Duodenum
30	chr12:57789800-57814600	Weak transcription	Fetal Muscle Trunk	muscle
31	chr12:57789800-57816000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr12:57789800-57816000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr12:57789800-57816200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr12:57790000-57810000	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr12:57790000-57813200	Weak transcription	Thymus	Thymus
36	chr12:57790000-57813600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr12:57790000-57814000	Weak transcription	Dnd41	blood
38	chr12:57790000-57814400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr12:57790000-57815400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr12:57790000-57815800	Weak transcription	Placenta	Placenta
41	chr12:57790000-57815800	Weak transcription	GM12878-XiMat	blood
42	chr12:57790000-57816200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr12:57790000-57823200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr12:57791000-57811800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr12:57795400-57809600	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr12:57795400-57810000	Weak transcription	K562	blood
47	chr12:57795400-57810200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr12:57795400-57812000	Weak transcription	NHEK	skin
49	chr12:57795400-57813400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr12:57795400-57816000	Weak transcription	Brain Angular Gyrus	brain

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