Variant report

Variant	rs11175656
Chromosome Location	chr12:40623755-40623756
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:40619170..40621140-chr12:40621940..40624766,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188906	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1031996	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs10748014	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10784381	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs10784386	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs10784428	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10878220	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10878222	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10878224	1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10878245	0.84[JPT][hapmap]
rs10878249	0.84[JPT][hapmap]
rs11175326	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs12827541	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1352876	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs1388591	0.84[JPT][hapmap]
rs1463719	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs1472118	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs1491927	0.81[ASN][1000 genomes]
rs1491931	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs1491938	0.83[JPT][hapmap]
rs1602578	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1844921	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1844922	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1948380	0.81[ASN][1000 genomes]
rs2170503	0.90[JPT][hapmap]
rs2248928	0.83[JPT][hapmap]
rs2249010	0.84[JPT][hapmap]
rs2249017	0.84[JPT][hapmap]
rs2404573	0.84[JPT][hapmap]
rs2404581	0.80[JPT][hapmap]
rs2638245	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2638249	0.81[ASN][1000 genomes]
rs2638254	0.86[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2638260	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs2638263	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs2638264	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs2638266	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs2638267	0.84[JPT][hapmap]
rs2708473	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs2708477	0.84[JPT][hapmap]
rs2708479	0.84[JPT][hapmap]
rs2708480	0.86[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2708481	0.83[JPT][hapmap]
rs2708485	0.81[ASN][1000 genomes]
rs2708491	0.81[ASN][1000 genomes]
rs2708492	0.81[ASN][1000 genomes]
rs2708493	0.81[ASN][1000 genomes]
rs2708494	0.80[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4360759	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs4767967	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4768221	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs716231	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs728622	0.81[ASN][1000 genomes]
rs728623	0.81[ASN][1000 genomes]
rs7306140	0.82[CHB][hapmap]
rs732374	0.85[JPT][hapmap]
rs7955902	0.84[JPT][hapmap]
rs878010	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs900253	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs937109	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs954884	0.85[JPT][hapmap]

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	nsv1044685	chr12:40574460-40771612	Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1052661	chr12:40603049-40642812	Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
3	nsv1045408	chr12:40620554-40664424	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11175656	SLC2A13	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40619400-40634600	Weak transcription	Spleen	Spleen
2	chr12:40619400-40644400	Weak transcription	Gastric	stomach
3	chr12:40619600-40636400	Weak transcription	Fetal Muscle Leg	muscle
4	chr12:40619600-40661000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr12:40619600-40678400	Weak transcription	Right Ventricle	heart
6	chr12:40619800-40658800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr12:40620400-40630000	Weak transcription	Ovary	ovary
8	chr12:40620400-40644200	Weak transcription	Brain Angular Gyrus	brain
9	chr12:40620800-40623800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr12:40620800-40626600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr12:40620800-40627600	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr12:40620800-40629200	Weak transcription	Stomach Mucosa	stomach
13	chr12:40620800-40629600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr12:40620800-40634800	Weak transcription	Lung	lung
15	chr12:40620800-40634800	Weak transcription	Pancreas	Pancrea
16	chr12:40620800-40644200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr12:40620800-40648000	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr12:40620800-40659200	Weak transcription	Brain Anterior Caudate	brain
19	chr12:40620800-40704200	Weak transcription	Esophagus	oesophagus
20	chr12:40621000-40629200	Weak transcription	Adipose Nuclei	Adipose
21	chr12:40621000-40630200	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr12:40621000-40632000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr12:40621000-40643800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr12:40621000-40659800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr12:40621000-40661200	Weak transcription	Rectal Smooth Muscle	rectum
26	chr12:40621200-40631800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr12:40621200-40632000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr12:40621400-40625800	Weak transcription	Fetal Kidney	kidney
29	chr12:40621400-40629000	Weak transcription	Aorta	Aorta
30	chr12:40621400-40632400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr12:40622000-40623800	Enhancers	A549	lung
32	chr12:40622400-40624400	Enhancers	Liver	Liver
33	chr12:40622800-40623800	Weak transcription	Primary B cells from peripheral blood	blood
34	chr12:40622800-40626400	Genic enhancers	Primary neutrophils fromperipheralblood	blood
35	chr12:40622800-40629200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr12:40622800-40661000	Weak transcription	Colon Smooth Muscle	Colon
37	chr12:40622800-40708800	Weak transcription	Left Ventricle	heart
38	chr12:40623000-40623800	Weak transcription	Right Atrium	heart
39	chr12:40623000-40624000	Active TSS	GM12878-XiMat	blood
40	chr12:40623200-40624000	Flanking Active TSS	Primary B cells from cord blood	blood
41	chr12:40623200-40624200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr12:40623600-40624000	Transcr. at gene 5' and 3'	Primary monocytes fromperipheralblood	blood
43	chr12:40623600-40624200	Active TSS	Pancreatic Islets	Pancreatic Islet

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