Variant report

Variant	rs13339152
Chromosome Location	chr16:12084047-12084048
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:12070396..12074345-chr16:12081594..12084708,4	MCF-7	breast:
2	chr16:12077520..12080777-chr16:12082061..12084894,3	MCF-7	breast:
3	chr16:12079547..12082011-chr16:12083989..12085646,2	K562	blood:

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

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs13332023	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13332654	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13334568	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs16958825	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16958827	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16958833	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2006256	1.00[ASN][1000 genomes]
rs2869492	0.85[CHB][hapmap]
rs365529	0.90[EUR][1000 genomes]
rs381584	0.87[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[TSI][hapmap]
rs3862447	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs405907	0.82[EUR][1000 genomes]
rs442332	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs448737	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs57196125	1.00[ASN][1000 genomes]
rs7189138	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7190848	0.86[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7199459	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs72784609	1.00[ASN][1000 genomes]
rs8052559	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[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	nsv1042660	chr16:11846873-12110435	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv571458	chr16:11925008-12087282	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12071400-12130800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr16:12071800-12088200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr16:12071800-12140200	Weak transcription	Fetal Intestine Small	intestine
4	chr16:12072000-12086200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr16:12072000-12087200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr16:12072000-12088200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr16:12072000-12093600	Weak transcription	Fetal Stomach	stomach
8	chr16:12072200-12084600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr16:12072200-12087400	Weak transcription	Fetal Thymus	thymus
10	chr16:12072200-12088200	Weak transcription	Duodenum Mucosa	Duodenum
11	chr16:12072200-12088200	Weak transcription	Right Ventricle	heart
12	chr16:12072200-12093800	Weak transcription	Thymus	Thymus
13	chr16:12072200-12096600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr16:12072200-12102600	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr16:12072400-12086200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr16:12072400-12086200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr16:12072400-12087200	Weak transcription	Primary T cells from cord blood	blood
18	chr16:12072400-12096400	Weak transcription	Ovary	ovary
19	chr16:12072400-12104400	Weak transcription	NHLF	lung
20	chr16:12072600-12086200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr16:12072600-12094000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr16:12072600-12094000	Weak transcription	Stomach Smooth Muscle	stomach
23	chr16:12072600-12099000	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr16:12072800-12102800	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr16:12074600-12088200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr16:12079600-12085800	Weak transcription	Lung	lung
27	chr16:12079600-12109600	Weak transcription	Gastric	stomach
28	chr16:12080200-12090000	Weak transcription	Aorta	Aorta
29	chr16:12080200-12093800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr16:12080400-12085000	Genic enhancers	Primary B cells from peripheral blood	blood
31	chr16:12080600-12088000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr16:12082000-12091400	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr16:12082000-12093000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr16:12082200-12085200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr16:12082200-12086000	Enhancers	Monocytes-CD14+_RO01746	blood
36	chr16:12082200-12087400	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr16:12082800-12084800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr16:12083000-12085200	Genic enhancers	GM12878-XiMat	blood
39	chr16:12083200-12084400	Enhancers	Left Ventricle	heart
40	chr16:12083200-12086800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr16:12083400-12085200	Enhancers	Fetal Kidney	kidney
42	chr16:12083400-12085800	Weak transcription	Pancreas	Pancrea
43	chr16:12083400-12086200	Weak transcription	Primary B cells from cord blood	blood
44	chr16:12083400-12102800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr16:12083600-12084200	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr16:12083600-12084600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr16:12083600-12086000	Weak transcription	Placenta	Placenta
48	chr16:12083600-12088400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr16:12083800-12084200	Enhancers	Brain Hippocampus Middle	brain
50	chr16:12083800-12084200	Enhancers	Brain Substantia Nigra	brain

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