Variant report

Variant	rs2662830
Chromosome Location	chr16:12133383-12133384
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:12068621..12072204-chr16:12129850..12134239,5	MCF-7	breast:

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

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1616017	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1616090	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1641835	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1641836	0.81[ASN][1000 genomes]
rs1641838	0.87[AMR][1000 genomes]
rs168409	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs168411	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1703492	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1703493	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1703494	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs171222	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1876708	0.80[ASN][1000 genomes]
rs2541581	0.82[ASN][1000 genomes]
rs2541582	0.83[ASN][1000 genomes]
rs2541583	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs350214	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs350215	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs350216	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs350218	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs350220	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs350221	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs350222	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7192491	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8055073	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs959665	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv977110	chr16:12123355-12146787	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12071800-12140200	Weak transcription	Fetal Intestine Small	intestine
2	chr16:12098400-12136000	Weak transcription	Fetal Stomach	stomach
3	chr16:12099600-12135200	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr16:12099600-12141200	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr16:12105200-12142200	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr16:12109800-12142200	Weak transcription	Gastric	stomach
7	chr16:12112000-12142200	Weak transcription	NHLF	lung
8	chr16:12112000-12144000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr16:12115200-12140600	Weak transcription	Thymus	Thymus
10	chr16:12116200-12141000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr16:12117200-12140400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr16:12117400-12183400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr16:12118200-12140400	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr16:12119200-12146400	Weak transcription	Fetal Lung	lung
15	chr16:12119400-12142000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr16:12119600-12148400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr16:12121000-12142200	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr16:12121400-12155000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr16:12121600-12140200	Weak transcription	Fetal Thymus	thymus
20	chr16:12121600-12142000	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr16:12121800-12140000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr16:12122200-12140200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr16:12122200-12140800	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr16:12122800-12144000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr16:12124400-12156600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr16:12124800-12136600	Weak transcription	Primary T cells from cord blood	blood
27	chr16:12124800-12142000	Weak transcription	Esophagus	oesophagus
28	chr16:12124800-12155000	Weak transcription	NH-A	brain
29	chr16:12125000-12140200	Weak transcription	Lung	lung
30	chr16:12125200-12136800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr16:12126400-12150000	Weak transcription	Small Intestine	intestine
32	chr16:12128200-12134000	Enhancers	Placenta	Placenta
33	chr16:12129000-12134000	Enhancers	Adipose Nuclei	Adipose
34	chr16:12129200-12133800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr16:12129600-12133800	Enhancers	Stomach Mucosa	stomach
36	chr16:12130000-12139800	Weak transcription	Liver	Liver
37	chr16:12130000-12142200	Weak transcription	Brain Angular Gyrus	brain
38	chr16:12130000-12153000	Weak transcription	Ovary	ovary
39	chr16:12130200-12142000	Weak transcription	Aorta	Aorta
40	chr16:12131000-12141600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr16:12131000-12142200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr16:12131200-12135200	Weak transcription	Spleen	Spleen
43	chr16:12131200-12136200	Weak transcription	Primary B cells from cord blood	blood
44	chr16:12131200-12139800	Weak transcription	Brain Hippocampus Middle	brain
45	chr16:12131200-12139800	Weak transcription	Right Ventricle	heart
46	chr16:12131200-12140200	Weak transcription	Brain Cingulate Gyrus	brain
47	chr16:12131200-12140600	Weak transcription	Fetal Muscle Leg	muscle
48	chr16:12131200-12141000	Weak transcription	GM12878-XiMat	blood
49	chr16:12131200-12142200	Weak transcription	Brain Anterior Caudate	brain
50	chr16:12131200-12142200	Weak transcription	Brain Substantia Nigra	brain

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