Variant report

Variant	rs59082884
Chromosome Location	chr1:46834249-46834250
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:46833928-46834290	K562	blood:	n/a	n/a
2	POLR2A	chr1:46833899-46836306	K562	blood:	n/a	n/a
3	POLR2A	chr1:46834220-46834349	Hela-S3	cervix:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:46831501..46834352-chr1:46851143..46853254,2	K562	blood:
2	chr1:46829128..46831471-chr1:46833892..46836194,2	MCF-7	breast:
3	chr1:46832831..46835765-chr1:46894196..46896899,2	K562	blood:
4	chr1:46806448..46808319-chr1:46834215..46835811,2	K562	blood:
5	chr1:46805343..46809669-chr1:46830716..46835811,6	K562	blood:
6	chr1:46833144..46835461-chr1:46838361..46840063,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000225779	TF binding region
ENSG00000117481	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10252	0.91[ASN][1000 genomes]
rs11211271	0.88[ASN][1000 genomes]
rs11802866	0.85[ASN][1000 genomes]
rs11804189	0.91[ASN][1000 genomes]
rs12073998	0.91[ASN][1000 genomes]
rs12075550	0.91[ASN][1000 genomes]
rs12562440	0.85[ASN][1000 genomes]
rs12563610	0.94[ASN][1000 genomes]
rs2145409	0.85[ASN][1000 genomes]
rs324416	0.83[ASN][1000 genomes]
rs3863641	0.91[ASN][1000 genomes]
rs3891758	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4110477	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs41293281	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41294484	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45480993	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs45540335	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs45564237	0.83[ASN][1000 genomes]
rs45577432	0.84[ASN][1000 genomes]
rs4660345	0.94[ASN][1000 genomes]
rs4660925	0.84[ASN][1000 genomes]
rs5013328	0.84[ASN][1000 genomes]
rs56733721	0.91[ASN][1000 genomes]
rs58710660	0.98[ASN][1000 genomes]
rs59411358	0.86[ASN][1000 genomes]
rs60519942	0.98[ASN][1000 genomes]
rs61221162	1.00[ASN][1000 genomes]
rs61784604	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs873978	0.83[ASN][1000 genomes]
rs913168	0.81[ASN][1000 genomes]
rs9865	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv829748	chr1:46724508-46876122	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv546162	chr1:46807597-46870761	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv1000562	chr1:46832451-47027044	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46807600-46835400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:46807600-46844600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:46807800-46835000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr1:46808600-46834600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr1:46809200-46848600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:46812600-46835200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr1:46813000-46835000	Strong transcription	Fetal Muscle Trunk	muscle
8	chr1:46813400-46834600	Strong transcription	Fetal Intestine Small	intestine
9	chr1:46814200-46834800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:46814600-46834400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:46815200-46835000	Strong transcription	Liver	Liver
12	chr1:46815200-46835200	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr1:46816800-46835800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr1:46818000-46834800	Strong transcription	Lung	lung
15	chr1:46818200-46834800	Strong transcription	Duodenum Mucosa	Duodenum
16	chr1:46818200-46834800	Strong transcription	Osteobl	bone
17	chr1:46818200-46839400	Strong transcription	Dnd41	blood
18	chr1:46820200-46834800	Strong transcription	Duodenum Smooth Muscle	Duodenum
19	chr1:46822200-46835800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:46823000-46834600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:46824600-46836200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:46826000-46834800	Strong transcription	Primary B cells from peripheral blood	blood
23	chr1:46826000-46834800	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr1:46826000-46834800	Strong transcription	Placenta	Placenta
25	chr1:46826200-46836000	Strong transcription	Primary B cells from cord blood	blood
26	chr1:46827400-46835200	Weak transcription	Stomach Mucosa	stomach
27	chr1:46827800-46837400	Weak transcription	Fetal Brain Male	brain
28	chr1:46828000-46835600	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr1:46828200-46836200	Weak transcription	Small Intestine	intestine
30	chr1:46828200-46836800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr1:46828200-46845400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:46828400-46835400	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr1:46828600-46843800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr1:46829000-46839800	Weak transcription	A549	lung
35	chr1:46829200-46835400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:46829200-46835800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr1:46829200-46836000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr1:46829200-46840200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:46829200-46840400	Weak transcription	Gastric	stomach
40	chr1:46829200-46846400	Weak transcription	Brain Cingulate Gyrus	brain
41	chr1:46829200-46847200	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr1:46829200-46847600	Weak transcription	Colon Smooth Muscle	Colon
43	chr1:46829200-46848000	Weak transcription	Ovary	ovary
44	chr1:46829400-46834600	Weak transcription	HepG2	liver
45	chr1:46829400-46834600	Weak transcription	HSMMtube	muscle
46	chr1:46829400-46835400	Weak transcription	HMEC	breast
47	chr1:46829400-46835800	Weak transcription	NH-A	brain
48	chr1:46829400-46837800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr1:46829400-46839000	Weak transcription	Brain Hippocampus Middle	brain
50	chr1:46829400-46859400	Weak transcription	Brain Substantia Nigra	brain

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