Variant report

Variant	rs58398910
Chromosome Location	chr16:12067268-12067269
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:12066859-12068666	GM12891	blood:	n/a	n/a
2	POLR2A	chr16:12067201-12067455	K562	blood:	n/a	n/a
3	POLR2A	chr16:12067239-12067429	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr16:12065945-12068722	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr16:12067080-12067335	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:12063141..12068645-chr16:12069062..12072358,5	K562	blood:
2	chr16:12065230..12068702-chr16:12068954..12072616,4	MCF-7	breast:
3	chr16:12054203..12056050-chr16:12064634..12067549,2	MCF-7	breast:
4	chr16:12008618..12010217-chr16:12066366..12068091,2	MCF-7	breast:
5	chr16:12065745..12068664-chr16:12070251..12071956,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000269121	TF binding region
UBL5P4	TF binding region
SNX29	TF binding region
ENSG00000048471	Chromatin interaction
ENSG00000234719	Chromatin interaction
ENSG00000103342	Chromatin interaction
ENSG00000260488	Chromatin interaction
ENSG00000266163	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10451099	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10468251	0.89[ASN][1000 genomes]
rs10852345	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10852346	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11075035	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11075036	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11075037	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11570137	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11570173	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11864397	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12597378	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12926535	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12927256	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12928141	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12929036	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12929544	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12929852	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12933691	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12934607	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2017662	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35965279	0.82[ASN][1000 genomes]
rs365423	0.87[ASN][1000 genomes]
rs366262	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3743591	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3851002	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3851003	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs387871	0.88[ASN][1000 genomes]
rs3916675	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57171695	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59320000	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6498255	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6498256	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6498257	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7189024	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7190636	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7191310	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7195514	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs72782778	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs8046211	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8047277	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8051343	0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs8055129	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8060611	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8062121	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9922422	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9922795	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	nsv962195	chr16:12053526-12071576	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12052200-12067600	Weak transcription	Osteobl	bone
2	chr16:12052200-12069600	Weak transcription	Primary T cells from cord blood	blood
3	chr16:12054600-12069400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr16:12056800-12069400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr16:12057000-12067600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr16:12057000-12067600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr16:12058800-12067600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr16:12058800-12069400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr16:12059000-12069400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr16:12059000-12069400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr16:12059000-12069400	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr16:12059200-12069400	Weak transcription	Adipose Nuclei	Adipose
13	chr16:12059400-12069400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr16:12059400-12069400	Weak transcription	NHEK	skin
15	chr16:12059400-12069600	Weak transcription	Brain Anterior Caudate	brain
16	chr16:12059400-12069600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr16:12059400-12069600	Weak transcription	Brain Substantia Nigra	brain
18	chr16:12059400-12069600	Weak transcription	HSMMtube	muscle
19	chr16:12059600-12069400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr16:12059600-12069600	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr16:12059800-12069600	Weak transcription	Fetal Thymus	thymus
22	chr16:12060000-12067600	Weak transcription	Left Ventricle	heart
23	chr16:12061600-12069400	Weak transcription	Pancreas	Pancrea
24	chr16:12061800-12069200	Weak transcription	K562	blood
25	chr16:12061800-12069600	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr16:12063600-12069400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr16:12064200-12069600	Weak transcription	Colonic Mucosa	Colon
28	chr16:12064400-12068800	Strong transcription	Fetal Stomach	stomach
29	chr16:12064800-12068400	Strong transcription	Thymus	Thymus
30	chr16:12065000-12069600	Weak transcription	Spleen	Spleen
31	chr16:12065200-12068600	Strong transcription	Primary B cells from peripheral blood	blood
32	chr16:12065200-12069600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr16:12065400-12068400	Strong transcription	Fetal Intestine Small	intestine
34	chr16:12065400-12069400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr16:12065600-12069400	Weak transcription	Primary B cells from cord blood	blood
36	chr16:12065800-12068400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr16:12065800-12069400	Weak transcription	Colon Smooth Muscle	Colon
38	chr16:12065800-12069600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr16:12066000-12067600	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr16:12066000-12069400	Weak transcription	Brain Germinal Matrix	brain
41	chr16:12066200-12069200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr16:12066200-12069200	Weak transcription	Placenta	Placenta
43	chr16:12066200-12069400	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr16:12066200-12069400	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr16:12066200-12069400	Weak transcription	GM12878-XiMat	blood
46	chr16:12066400-12067800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr16:12066400-12067800	Weak transcription	HepG2	liver
48	chr16:12066400-12069400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr16:12066400-12069400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr16:12066400-12069400	Weak transcription	Fetal Brain Female	brain

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