Variant report

Variant	rs16998873
Chromosome Location	chr20:52678146-52678147
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52212827..52216446-chr20:52677595..52681391,3	MCF-7	breast:
2	chr20:52676834..52679503-chr20:53266669..53268779,2	MCF-7	breast:
3	chr20:45986431..45988883-chr20:52677453..52680110,2	MCF-7	breast:
4	chr20:52677507..52680494-chr3:64381929..64383896,2	MCF-7	breast:
5	chr20:41005640..41008273-chr20:52676406..52679770,3	MCF-7	breast:
6	chr20:52674058..52677861-chr20:52678021..52680977,4	K562	blood:
7	chr20:52675939..52678149-chr20:53262263..53264864,2	MCF-7	breast:
8	chr17:59488569..59490158-chr20:52676107..52678270,2	MCF-7	breast:
9	chr20:46750253..46752428-chr20:52678041..52680092,2	MCF-7	breast:
10	chr20:52556569..52566193-chr20:52677353..52682397,12	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000267280	Chromatin interaction
ENSG00000236352	Chromatin interaction
ENSG00000187013	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs12624475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12624494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12624748	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12624750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12625278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12625283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16998867	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16998871	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16998886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2020975	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2107328	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2870305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2870306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34522098	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3787540	0.85[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3787544	0.85[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3787545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3787546	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3787551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs41304655	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs41308729	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58634156	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60949012	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6123346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6123348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6123349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6123350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6123351	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6123352	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6123353	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6123354	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6123355	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6123356	1.00[ASW][hapmap];0.94[CHB][hapmap];0.80[TSI][hapmap]
rs6127074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6127075	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6127076	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6127078	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6127079	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6127080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6127081	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6127083	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6127084	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs6127085	1.00[ASW][hapmap];0.89[CHB][hapmap];0.83[GIH][hapmap];0.82[MEX][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6127086	0.89[CHB][hapmap];1.00[YRI][hapmap]
rs6127088	1.00[ASW][hapmap];0.94[CHB][hapmap];1.00[YRI][hapmap]
rs6127090	1.00[YRI][hapmap]
rs66461137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66470134	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66593006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67341659	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68072066	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73134888	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs899049	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases
2	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16998873	ZFP30	trans	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52645200-52682200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr20:52669400-52681800	Weak transcription	Gastric	stomach
3	chr20:52674400-52681200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr20:52674400-52682000	Weak transcription	Colonic Mucosa	Colon
5	chr20:52675000-52683000	Weak transcription	HepG2	liver
6	chr20:52675200-52678800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr20:52675400-52679200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr20:52675600-52679200	Weak transcription	K562	blood
9	chr20:52675600-52679600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr20:52675800-52679600	Weak transcription	Primary B cells from peripheral blood	blood
11	chr20:52676800-52679200	Weak transcription	GM12878-XiMat	blood
12	chr20:52677200-52680000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr20:52677400-52680200	Enhancers	Stomach Mucosa	stomach
14	chr20:52677600-52678200	Enhancers	Fetal Stomach	stomach
15	chr20:52677600-52678600	Enhancers	NHEK	skin
16	chr20:52677600-52678800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr20:52677600-52678800	Enhancers	Muscle Satellite Cultured Cells	--
18	chr20:52677600-52679400	Enhancers	HSMM	muscle
19	chr20:52677600-52679400	Enhancers	NH-A	brain
20	chr20:52677600-52679400	Enhancers	Osteobl	bone
21	chr20:52677600-52679800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr20:52677600-52679800	Enhancers	HSMMtube	muscle
23	chr20:52677600-52679800	Enhancers	NHDF-Ad	bronchial
24	chr20:52677800-52678200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr20:52677800-52678200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr20:52677800-52678200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr20:52677800-52678200	Enhancers	HMEC	breast
28	chr20:52677800-52678400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr20:52677800-52678400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr20:52677800-52678600	Enhancers	Brain Hippocampus Middle	brain
31	chr20:52677800-52678600	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr20:52677800-52679400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr20:52677800-52679800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr20:52677800-52679800	Enhancers	Brain Cingulate Gyrus	brain
35	chr20:52677800-52679800	Enhancers	Brain Substantia Nigra	brain
36	chr20:52677800-52680000	Enhancers	Adipose Nuclei	Adipose
37	chr20:52678000-52678200	Enhancers	Fetal Muscle Leg	muscle
38	chr20:52678000-52678600	Enhancers	Brain Angular Gyrus	brain
39	chr20:52678000-52678600	Enhancers	A549	lung
40	chr20:52678000-52679800	Enhancers	Fetal Heart	heart

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