Variant report

Variant	rs62028253
Chromosome Location	chr16:12652996-12652997
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:12651809..12653725-chr16:12657374..12659013,2	MCF-7	breast:
2	chr16:12652319..12653186-chr16:12913152..12913807,2	MCF-7	breast:
3	chr16:12646912..12648633-chr16:12652435..12654729,2	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11639553	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11642881	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11643010	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11643162	0.81[AMR][1000 genomes]
rs11644221	0.81[AMR][1000 genomes]
rs11645658	0.90[AMR][1000 genomes]
rs11646569	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11646611	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11647633	0.90[AMR][1000 genomes]
rs11648724	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12148951	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12149441	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12325256	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17223249	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17223442	0.90[AMR][1000 genomes]
rs17821897	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2042915	0.96[ASN][1000 genomes]
rs2856784	0.85[EUR][1000 genomes]
rs34147303	0.83[AMR][1000 genomes]
rs55645382	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55779146	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55910004	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56013945	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62028254	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62028663	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62028664	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62028744	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62028746	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62028749	0.88[AMR][1000 genomes]
rs7187812	0.85[EUR][1000 genomes]
rs7188575	0.96[EUR][1000 genomes]
rs7190533	0.81[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs7191878	0.81[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs7195739	0.81[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs7197122	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9452	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv571463	chr16:12367791-12783535	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1051242	chr16:12482972-12897243	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv542749	chr16:12482972-12897243	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv1035581	chr16:12516946-12863700	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1051607	chr16:12522130-13347676	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv542750	chr16:12522130-13347676	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv431433	chr16:12628409-12654408	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv1842867	chr16:12632286-12678721	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	esv2751546	chr16:12635498-12674704	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv1050004	chr16:12641649-12654618	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	esv2757628	chr16:12647181-12654408	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
13	esv2758630	chr16:12647181-12654408	Enhancers Weak transcription Strong transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
14	esv2760409	chr16:12647181-12654504	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
15	nsv431434	chr16:12648058-12654408	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
16	nsv1050925	chr16:12648058-12670588	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv1044772	chr16:12648266-12668751	ZNF genes & repeats Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12613000-12670800	Weak transcription	Pancreas	Pancrea
2	chr16:12632800-12663800	Weak transcription	Aorta	Aorta
3	chr16:12633400-12654400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr16:12639400-12659000	Weak transcription	Lung	lung
5	chr16:12641200-12667000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr16:12642000-12662200	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr16:12642200-12655000	Weak transcription	Spleen	Spleen
8	chr16:12642400-12653000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr16:12643000-12659200	Weak transcription	Placenta	Placenta
10	chr16:12643200-12653000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr16:12645200-12661600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr16:12646000-12655400	Weak transcription	Gastric	stomach
13	chr16:12646000-12659000	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr16:12646000-12661000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr16:12646200-12654800	Weak transcription	Primary T cells from cord blood	blood
16	chr16:12646200-12659800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr16:12646200-12660000	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr16:12646400-12659400	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr16:12646400-12660800	Weak transcription	Thymus	Thymus
20	chr16:12647400-12658800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr16:12647400-12662200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr16:12647400-12665200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr16:12647600-12661600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr16:12648000-12653000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr16:12648000-12662200	Weak transcription	Fetal Stomach	stomach
26	chr16:12648400-12668800	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr16:12648800-12659200	Weak transcription	Esophagus	oesophagus
28	chr16:12649000-12658600	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr16:12649800-12662200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr16:12651000-12653200	Enhancers	Brain Hippocampus Middle	brain
31	chr16:12652000-12654400	Weak transcription	GM12878-XiMat	blood
32	chr16:12652200-12660200	Strong transcription	Primary B cells from cord blood	blood
33	chr16:12652200-12669200	Weak transcription	Brain Cingulate Gyrus	brain
34	chr16:12652400-12658200	Strong transcription	Primary B cells from peripheral blood	blood
35	chr16:12652400-12666400	Weak transcription	Brain Anterior Caudate	brain
36	chr16:12652600-12665800	Weak transcription	Brain Angular Gyrus	brain
37	chr16:12652600-12672200	Weak transcription	Right Ventricle	heart
38	chr16:12652800-12653200	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr16:12652800-12653600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr16:12652800-12653800	Enhancers	NHDF-Ad	bronchial
41	chr16:12652800-12663400	Weak transcription	Brain Substantia Nigra	brain

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