Variant report

Variant	rs11111803
Chromosome Location	chr12:104221467-104221468
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104221407..104223311-chr12:104252551..104254594,2	MCF-7	breast:
2	chr12:104214519..104222192-chr12:104231005..104236989,8	K562	blood:
3	chr12:104219162..104221997-chr12:104232338..104234895,2	K562	blood:
4	chr12:104221267..104222834-chr12:104227996..104230491,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111696	Chromatin interaction
ENSG00000257327	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10082821	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861110	0.93[CEU][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10861111	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10861113	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10861114	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10861115	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861116	0.93[CEU][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10861117	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10861118	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861119	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111760	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11111780	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11111790	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111794	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111797	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11111806	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11111807	0.96[EUR][1000 genomes]
rs12299784	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12313259	0.93[CEU][hapmap];0.97[TSI][hapmap]
rs12320424	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12368209	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12369835	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12426059	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs1370782	0.93[CEU][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1370783	0.95[EUR][1000 genomes]
rs17034657	0.93[CEU][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs3087891	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4964197	0.93[CEU][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4964540	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4964571	0.93[CEU][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4964574	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4964605	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4964787	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6539102	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7138889	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7315948	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73175816	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]

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	esv34031	chr12:104114277-104298546	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11111803	NT5DC3	cis	Whole Blood	GTEx
rs11111803	IGF1	cis	parietal	SCAN
rs11111803	TU12B1-TY	cis	multi-tissue	Pritchard
rs11111803	RP11-341G23.4	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104196400-104221800	Weak transcription	Brain Anterior Caudate	brain
2	chr12:104208200-104221800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr12:104208200-104223200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr12:104208200-104227800	Weak transcription	Pancreas	Pancrea
5	chr12:104208800-104227600	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr12:104215200-104221800	Weak transcription	Aorta	Aorta
7	chr12:104215200-104226000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr12:104215200-104227600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr12:104215400-104221600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr12:104215400-104221600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr12:104215400-104221600	Weak transcription	HepG2	liver
12	chr12:104215400-104221800	Weak transcription	Brain Angular Gyrus	brain
13	chr12:104215400-104223400	Enhancers	Rectal Smooth Muscle	rectum
14	chr12:104215800-104221600	Weak transcription	NHLF	lung
15	chr12:104216400-104221600	Weak transcription	HSMM	muscle
16	chr12:104216600-104221600	Weak transcription	HMEC	breast
17	chr12:104216600-104221800	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr12:104216600-104221800	Weak transcription	NHEK	skin
19	chr12:104216600-104227800	Weak transcription	NH-A	brain
20	chr12:104217800-104222000	Weak transcription	Fetal Muscle Leg	muscle
21	chr12:104218400-104221600	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr12:104218400-104221800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr12:104218400-104224800	Weak transcription	K562	blood
24	chr12:104218400-104233000	Weak transcription	Gastric	stomach
25	chr12:104218400-104233400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr12:104218800-104227400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr12:104218800-104232800	Weak transcription	Psoas Muscle	Psoas
28	chr12:104219000-104221800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr12:104219000-104221800	Weak transcription	Osteobl	bone
30	chr12:104219000-104222000	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr12:104219600-104221800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr12:104219600-104226400	Weak transcription	Ovary	ovary
33	chr12:104219800-104221800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr12:104220000-104221800	Weak transcription	Stomach Smooth Muscle	stomach
35	chr12:104220000-104232000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr12:104220200-104221800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr12:104220400-104221600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr12:104220400-104222000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr12:104220600-104221600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr12:104220600-104222600	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr12:104221200-104221600	Enhancers	Monocytes-CD14+_RO01746	blood
42	chr12:104221200-104222000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr12:104221200-104222200	Enhancers	A549	lung
44	chr12:104221200-104224200	Enhancers	Colon Smooth Muscle	Colon
45	chr12:104221400-104221600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr12:104221400-104222200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr12:104221400-104222200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr12:104221400-104223400	Enhancers	Muscle Satellite Cultured Cells	--
49	chr12:104221400-104223600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr12:104221400-104228200	Enhancers	Primary monocytes fromperipheralblood	blood

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