Variant report

Variant	rs11648404
Chromosome Location	chr16:12115943-12115944
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:12069225..12071797-chr16:12115611..12118590,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234719	Chromatin interaction
ENSG00000048471	Chromatin interaction
ENSG00000260488	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11648938	1.00[CEU][hapmap]
rs2869492	0.92[CEU][hapmap]
rs8045634	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs8050827	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs8051278	0.82[CHB][hapmap]
rs8051349	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.97[YRI][hapmap]
rs8062691	1.00[CEU][hapmap];0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv905347	chr16:12010444-12243329	Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv482458	chr16:12014925-12145977	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1043959	chr16:12039346-12285269	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs11648404	RP11-166B2.1	cis	Thyroid	GTEx
rs11648404	RP11-166B2.1	cis	Nerve Tibial	GTEx
rs11648404	RP11-166B2.1	cis	Skin Sun Exposed Lower leg	GTEx
rs11648404	RP11-166B2.1	cis	Esophagus Muscularis	GTEx
rs11648404	RP11-166B2.1	cis	Heart Left Ventricle	GTEx
rs11648404	RP11-166B2.1	cis	Stomach	GTEx
rs11648404	RP11-166B2.1	cis	Artery Aorta	GTEx
rs11648404	RP11-166B2.1	cis	Artery Tibial	GTEx
rs11648404	RP11-166B2.1	cis	Adipose Subcutaneous	GTEx
rs11648404	RP11-166B2.1	cis	Whole Blood	GTEx

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12071400-12130800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr16:12071800-12140200	Weak transcription	Fetal Intestine Small	intestine
3	chr16:12085400-12118200	Weak transcription	Esophagus	oesophagus
4	chr16:12098400-12136000	Weak transcription	Fetal Stomach	stomach
5	chr16:12098600-12118200	Weak transcription	Pancreas	Pancrea
6	chr16:12099400-12118400	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr16:12099600-12135200	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr16:12099600-12141200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr16:12101800-12121400	Weak transcription	Stomach Smooth Muscle	stomach
10	chr16:12101800-12123600	Weak transcription	Lung	lung
11	chr16:12101800-12129800	Weak transcription	Aorta	Aorta
12	chr16:12102000-12124200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr16:12104600-12116400	Weak transcription	Brain Hippocampus Middle	brain
14	chr16:12105000-12120600	Weak transcription	Brain Substantia Nigra	brain
15	chr16:12105200-12142200	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr16:12105400-12120800	Weak transcription	Fetal Thymus	thymus
17	chr16:12105800-12120800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr16:12105800-12124200	Weak transcription	Primary T cells from cord blood	blood
19	chr16:12108400-12119400	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr16:12108600-12128400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr16:12109800-12118200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr16:12109800-12124200	Weak transcription	Left Ventricle	heart
23	chr16:12109800-12142200	Weak transcription	Gastric	stomach
24	chr16:12110000-12118400	Enhancers	Primary B cells from peripheral blood	blood
25	chr16:12110400-12118200	Enhancers	Primary B cells from cord blood	blood
26	chr16:12110600-12119600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr16:12110800-12119400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr16:12111000-12117400	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr16:12111000-12119200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr16:12111000-12119400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr16:12112000-12118000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr16:12112000-12118400	Weak transcription	NHDF-Ad	bronchial
33	chr16:12112000-12120800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr16:12112000-12124200	Weak transcription	HSMMtube	muscle
35	chr16:12112000-12129200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr16:12112000-12142200	Weak transcription	NHLF	lung
37	chr16:12112000-12144000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr16:12113200-12129200	Weak transcription	Ovary	ovary
39	chr16:12113400-12118200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr16:12114200-12120800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr16:12114800-12116200	Enhancers	Primary hematopoietic stem cells	blood
42	chr16:12115200-12118600	Genic enhancers	GM12878-XiMat	blood
43	chr16:12115200-12140600	Weak transcription	Thymus	Thymus
44	chr16:12115400-12116000	Enhancers	Adipose Nuclei	Adipose
45	chr16:12115400-12116200	Enhancers	Placenta	Placenta
46	chr16:12115800-12116000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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