Variant report

Variant	rs58678671
Chromosome Location	chr1:45094479-45094480
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PBX3	chr1:45094414-45095315	SK-N-SH	brain:	n/a	n/a
2	TCF12	chr1:45094307-45095441	SK-N-SH	brain:	n/a	n/a
3	TCF12	chr1:45094366-45095465	SK-N-SH	brain:	n/a	n/a
4	GATA3	chr1:45094405-45095474	SK-N-SH	brain:	n/a	n/a
5	PBX3	chr1:45094437-45095321	SK-N-SH	brain:	n/a	n/a
6	NFIC	chr1:45094453-45095375	SK-N-SH	brain:	n/a	n/a
7	RXRA	chr1:45094374-45095318	SK-N-SH	brain:	n/a	n/a
8	GATA3	chr1:45094448-45095402	SK-N-SH	brain:	n/a	n/a
9	NFIC	chr1:45094455-45095021	SK-N-SH	brain:	n/a	n/a
10	NR2F2	chr1:45094466-45095373	MCF-7	breast:	n/a	chr1:45094529-45094544
11	FOSL2	chr1:45094477-45095321	SK-N-SH	brain:	n/a	chr1:45095118-45095129 chr1:45095117-45095125
12	GATA3	chr1:45094423-45095485	MCF-7	breast:	n/a	n/a
13	RCOR1	chr1:45093921-45098862	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:44689798..44691974-chr1:45093885..45095737,2	K562	blood:
2	chr1:45086647..45106769-chr1:45179099..45192041,56	K562	blood:

Variant related genes	Relation type
RNF220	TF binding region
ENSG00000199377	Chromatin interaction
ENSG00000198520	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1051664	0.99[ASN][1000 genomes]
rs1135319	1.00[EUR][1000 genomes]
rs56257701	0.97[ASN][1000 genomes]
rs58019041	0.97[ASN][1000 genomes]
rs58035624	0.93[ASN][1000 genomes]
rs58401148	0.97[ASN][1000 genomes]
rs59370761	0.97[ASN][1000 genomes]
rs59764933	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59790609	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60469789	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs60476008	0.80[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6429544	0.94[ASN][1000 genomes]
rs6665374	0.93[ASN][1000 genomes]
rs6667593	0.97[ASN][1000 genomes]
rs6698388	0.99[ASN][1000 genomes]
rs72671972	0.97[ASN][1000 genomes]
rs74070566	0.94[ASN][1000 genomes]
rs74070577	0.97[ASN][1000 genomes]
rs7539312	0.93[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	nsv533037	chr1:44361728-45333408	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv1004861	chr1:44843654-45210176	Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
3	nsv534940	chr1:44843654-45210176	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
4	nsv461395	chr1:44898998-45119965	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
5	nsv546144	chr1:44898998-45119965	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
6	nsv998476	chr1:45001278-45311757	Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
7	nsv534941	chr1:45001278-45311757	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45074800-45096800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr1:45079600-45096800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:45083000-45097000	Weak transcription	Spleen	Spleen
4	chr1:45083400-45097200	Weak transcription	Gastric	stomach
5	chr1:45083600-45097000	Weak transcription	Right Atrium	heart
6	chr1:45083800-45096600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:45083800-45096600	Weak transcription	Fetal Heart	heart
8	chr1:45084200-45097000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:45084800-45096800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:45085600-45097000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:45085600-45097000	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr1:45085800-45096600	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr1:45085800-45096800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr1:45087200-45096800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr1:45087600-45096600	Weak transcription	Brain Angular Gyrus	brain
16	chr1:45087800-45096400	Weak transcription	Brain Anterior Caudate	brain
17	chr1:45087800-45096800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr1:45088400-45094600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr1:45089800-45097000	Weak transcription	Psoas Muscle	Psoas
20	chr1:45090800-45096800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:45091000-45096600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:45091400-45097000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr1:45091400-45097000	Weak transcription	Fetal Muscle Trunk	muscle
24	chr1:45091600-45096600	Weak transcription	Fetal Muscle Leg	muscle
25	chr1:45091800-45096200	Strong transcription	Brain Hippocampus Middle	brain
26	chr1:45091800-45096400	Strong transcription	Brain Cingulate Gyrus	brain
27	chr1:45091800-45097000	Weak transcription	Fetal Brain Female	brain
28	chr1:45092000-45096800	Weak transcription	Fetal Brain Male	brain
29	chr1:45092000-45097000	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr1:45092200-45094800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:45093200-45097000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr1:45093400-45094600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:45093600-45096600	Enhancers	K562	blood
34	chr1:45093600-45097200	Enhancers	NHLF	lung
35	chr1:45093800-45095200	Strong transcription	Brain Substantia Nigra	brain
36	chr1:45093800-45097200	Enhancers	NHDF-Ad	bronchial
37	chr1:45094000-45096800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr1:45094000-45096800	Weak transcription	Primary B cells from cord blood	blood
39	chr1:45094000-45097000	Enhancers	Osteobl	bone
40	chr1:45094200-45095800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr1:45094200-45097000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr1:45094400-45094600	Enhancers	Hela-S3	cervix
43	chr1:45094400-45095400	Enhancers	NHEK	skin
44	chr1:45094400-45095600	Enhancers	Muscle Satellite Cultured Cells	--
45	chr1:45094400-45095600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr1:45094400-45095800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:45094400-45096200	Enhancers	NH-A	brain

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