Variant report

Variant	rs350222
Chromosome Location	chr16:12121579-12121580
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:12070262..12072068-chr16:12120088..12123053,3	MCF-7	breast:

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

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12922317	0.91[CEU][hapmap]
rs1616017	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1616090	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1641835	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs168409	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs168411	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1703492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1703493	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1703494	0.85[AMR][1000 genomes]
rs171222	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2541583	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2662829	0.82[CHB][hapmap]
rs2662830	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs350214	0.84[AMR][1000 genomes]
rs350215	0.83[AMR][1000 genomes]
rs350216	0.83[AMR][1000 genomes]
rs350220	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs350221	0.91[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes]
rs3851005	0.87[CEU][hapmap]
rs7192491	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs8043644	0.87[CEU][hapmap]
rs8055073	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8061496	0.88[CEU][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

No data

Chromatin state (count:77 , 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	chr16:12071800-12140200	Weak transcription	Fetal Intestine Small	intestine
3	chr16:12098400-12136000	Weak transcription	Fetal Stomach	stomach
4	chr16:12099600-12135200	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr16:12099600-12141200	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr16:12101800-12123600	Weak transcription	Lung	lung
7	chr16:12101800-12129800	Weak transcription	Aorta	Aorta
8	chr16:12102000-12124200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr16:12105200-12142200	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr16:12105800-12124200	Weak transcription	Primary T cells from cord blood	blood
11	chr16:12108600-12128400	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr16:12109800-12124200	Weak transcription	Left Ventricle	heart
13	chr16:12109800-12142200	Weak transcription	Gastric	stomach
14	chr16:12112000-12124200	Weak transcription	HSMMtube	muscle
15	chr16:12112000-12129200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr16:12112000-12142200	Weak transcription	NHLF	lung
17	chr16:12112000-12144000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr16:12113200-12129200	Weak transcription	Ovary	ovary
19	chr16:12115200-12140600	Weak transcription	Thymus	Thymus
20	chr16:12116200-12141000	Weak transcription	Primary hematopoietic stem cells	blood
21	chr16:12116800-12129600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr16:12116800-12130800	Weak transcription	Fetal Kidney	kidney
23	chr16:12117200-12140400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr16:12117400-12183400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr16:12118200-12140400	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr16:12118400-12121600	Genic enhancers	Primary B cells from peripheral blood	blood
27	chr16:12118400-12130800	Weak transcription	Right Ventricle	heart
28	chr16:12118600-12129400	Weak transcription	NHDF-Ad	bronchial
29	chr16:12118600-12130800	Weak transcription	Duodenum Mucosa	Duodenum
30	chr16:12118600-12130800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr16:12118800-12128400	Weak transcription	Adipose Nuclei	Adipose
32	chr16:12118800-12129600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr16:12119200-12146400	Weak transcription	Fetal Lung	lung
34	chr16:12119400-12121600	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr16:12119400-12129600	Weak transcription	Stomach Mucosa	stomach
36	chr16:12119400-12142000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr16:12119600-12121600	Enhancers	Fetal Brain Male	brain
38	chr16:12119600-12130800	Weak transcription	Pancreas	Pancrea
39	chr16:12119600-12148400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr16:12119800-12130800	Weak transcription	HepG2	liver
41	chr16:12120000-12121600	Enhancers	Brain Hippocampus Middle	brain
42	chr16:12120200-12121600	Enhancers	Fetal Brain Female	brain
43	chr16:12120200-12132600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr16:12120400-12123800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr16:12120400-12128200	Weak transcription	Placenta	Placenta
46	chr16:12120600-12124200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr16:12120800-12121600	Enhancers	Fetal Thymus	thymus
48	chr16:12120800-12121800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr16:12120800-12121800	Flanking Active TSS	HMEC	breast
50	chr16:12120800-12122000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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