Variant report

Variant	rs61839258
Chromosome Location	chr10:18689638-18689639
allele	A/C/G/T
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	GATA3	chr10:18689156-18689710	MCF-7	breast:	n/a	chr10:18689513-18689522 chr10:18689515-18689525 chr10:18689510-18689526 chr10:18689515-18689522
2	CUX1	chr10:18689193-18689736	GM12878	blood:	n/a	n/a
3	RCOR1	chr10:18687837-18689826	GM12878	blood:	n/a	n/a
4	GATA3	chr10:18689035-18690088	MCF-7	breast:	n/a	chr10:18689513-18689522 chr10:18689515-18689525 chr10:18689510-18689526 chr10:18689515-18689522
5	GATA3	chr10:18689303-18689708	MCF-7	breast:	n/a	chr10:18689513-18689522 chr10:18689515-18689525 chr10:18689510-18689526 chr10:18689515-18689522
6	NR2F2	chr10:18689295-18689707	MCF-7	breast:	n/a	n/a
7	POLR2A	chr10:18689174-18690281	GM19193	blood:	n/a	n/a
8	GATA3	chr10:18689314-18689711	A549	lung:	n/a	chr10:18689513-18689522 chr10:18689515-18689525 chr10:18689510-18689526 chr10:18689515-18689522
9	GATA2	chr10:18689245-18690198	SH-SY5Y	brain:	n/a	chr10:18689513-18689522 chr10:18689515-18689525 chr10:18689510-18689526 chr10:18689515-18689522
10	ZNF384	chr10:18689454-18689666	K562	blood:	n/a	n/a
11	BHLHE40	chr10:18689030-18689643	GM12878	blood:	n/a	n/a
12	TBP	chr10:18687963-18690197	GM12878	blood:	n/a	n/a
13	MAZ	chr10:18689258-18689899	GM12878	blood:	n/a	chr10:18689487-18689497
14	NR2F2	chr10:18689249-18689839	MCF-7	breast:	n/a	n/a
15	REST	chr10:18688933-18690209	H1-neurons	neurons:	n/a	chr10:18689474-18689487 chr10:18689873-18689881
16	RFX5	chr10:18689089-18689697	GM12878	blood:	n/a	n/a
17	MAZ	chr10:18689376-18689648	HepG2	liver:	n/a	chr10:18689487-18689497
18	EP300	chr10:18689040-18689932	GM12878	blood:	n/a	chr10:18689572-18689586 chr10:18689570-18689584 chr10:18689304-18689318 chr10:18689805-18689818 chr10:18689571-18689585
19	ZNF263	chr10:18689116-18690193	HEK293-T-REx	kidney:	n/a	chr10:18689474-18689483 chr10:18689473-18689494
20	EP300	chr10:18688888-18689790	GM12878	blood:	n/a	chr10:18689572-18689586 chr10:18689570-18689584 chr10:18689304-18689318 chr10:18689571-18689585
21	KAP1	chr10:18689024-18689948	U2OS	brain:	n/a	n/a
22	POLR2A	chr10:18689072-18689690	H1-neurons	neurons:	n/a	n/a
23	GATA3	chr10:18689240-18689826	SH-SY5Y	brain:	n/a	chr10:18689513-18689522 chr10:18689515-18689525 chr10:18689510-18689526 chr10:18689515-18689522
24	USF2	chr10:18689171-18689831	GM12878	blood:	n/a	n/a
25	MAX	chr10:18689178-18689654	GM12878	blood:	n/a	chr10:18689487-18689497
26	CHD2	chr10:18689011-18689698	GM12878	blood:	n/a	chr10:18689485-18689495
27	MXI1	chr10:18688888-18689643	GM12878	blood:	n/a	n/a
28	GATA3	chr10:18689372-18689675	MCF-7	breast:	n/a	chr10:18689513-18689522 chr10:18689515-18689525 chr10:18689510-18689526 chr10:18689515-18689522
29	MAZ	chr10:18688944-18689761	IMR90	lung:	n/a	chr10:18689487-18689497
30	GATA3	chr10:18689124-18689908	A549	lung:	n/a	chr10:18689513-18689522 chr10:18689515-18689525 chr10:18689510-18689526 chr10:18689515-18689522
31	GATA3	chr10:18689186-18689875	SK-N-SH	brain:	n/a	chr10:18689513-18689522 chr10:18689515-18689525 chr10:18689510-18689526 chr10:18689515-18689522
32	GATA3	chr10:18689304-18689694	T-47D	breast:	n/a	chr10:18689513-18689522 chr10:18689515-18689525 chr10:18689510-18689526 chr10:18689515-18689522
33	ZNF384	chr10:18689179-18689989	GM12878	blood:	n/a	n/a
34	EBF1	chr10:18688878-18690003	GM12878	blood:	n/a	chr10:18689796-18689807
35	GATA3	chr10:18689163-18689896	SK-N-SH	brain:	n/a	chr10:18689513-18689522 chr10:18689515-18689525 chr10:18689510-18689526 chr10:18689515-18689522
36	CHD1	chr10:18688957-18690088	GM12878	blood:	n/a	chr10:18689485-18689495 chr10:18689943-18689950

Variant related genes	Relation type
CACNB2	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11014026	0.87[AMR][1000 genomes]
rs11014084	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11014144	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11014156	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11014175	0.85[ASN][1000 genomes]
rs11014188	0.85[ASN][1000 genomes]
rs11014208	0.85[ASN][1000 genomes]
rs11014210	0.85[ASN][1000 genomes]
rs11014211	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12049663	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16917251	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17690664	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3829133	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61839230	0.89[AMR][1000 genomes]
rs61839231	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs61841960	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61842001	0.80[ASN][1000 genomes]
rs6482438	0.85[ASN][1000 genomes]
rs7096168	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72786093	0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv550042	chr10:18683267-18994583	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18688800-18691800	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr10:18689000-18689800	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr10:18689000-18689800	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr10:18689000-18689800	Active TSS	Brain Substantia Nigra	brain
5	chr10:18689000-18690000	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr10:18689000-18690000	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr10:18689000-18690000	Flanking Bivalent TSS/Enh	A549	lung
8	chr10:18689000-18690200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
9	chr10:18689000-18690200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
10	chr10:18689000-18690200	Active TSS	Brain Hippocampus Middle	brain
11	chr10:18689000-18690200	Active TSS	Fetal Brain Female	brain
12	chr10:18689000-18690400	Active TSS	Fetal Intestine Small	intestine
13	chr10:18689000-18690600	Active TSS	Fetal Intestine Large	intestine
14	chr10:18689000-18691000	Active TSS	Brain Angular Gyrus	brain
15	chr10:18689000-18691000	Active TSS	Brain Cingulate Gyrus	brain
16	chr10:18689000-18691000	Active TSS	Rectal Smooth Muscle	rectum
17	chr10:18689000-18691200	Active TSS	Colonic Mucosa	Colon
18	chr10:18689000-18691800	Active TSS	Rectal Mucosa Donor 31	rectum
19	chr10:18689000-18692600	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr10:18689200-18689800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr10:18689200-18689800	Active TSS	H1 Cell Line	embryonic stem cell
22	chr10:18689200-18689800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr10:18689200-18689800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr10:18689200-18689800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr10:18689200-18689800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr10:18689200-18689800	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
27	chr10:18689200-18689800	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr10:18689200-18689800	Flanking Active TSS	Fetal Brain Male	brain
29	chr10:18689200-18689800	Active TSS	Fetal Muscle Leg	muscle
30	chr10:18689200-18689800	Active TSS	Fetal Stomach	stomach
31	chr10:18689200-18690000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr10:18689200-18690000	Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr10:18689200-18690000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr10:18689200-18690000	Active TSS	Aorta	Aorta
35	chr10:18689200-18690000	Active TSS	Fetal Kidney	kidney
36	chr10:18689200-18690000	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
37	chr10:18689200-18690000	Active TSS	Thymus	Thymus
38	chr10:18689200-18690000	Active TSS	NHLF	lung
39	chr10:18689200-18690200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
40	chr10:18689200-18690200	Active TSS	H9 Cell Line	embryonic stem cell
41	chr10:18689200-18690200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
42	chr10:18689200-18690200	Active TSS	Primary hematopoietic stem cells	blood
43	chr10:18689200-18690200	Active TSS	Skeletal Muscle Female	skeletal muscle
44	chr10:18689200-18690400	Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr10:18689200-18690600	Enhancers	Stomach Smooth Muscle	stomach
46	chr10:18689200-18691600	Weak transcription	Small Intestine	intestine
47	chr10:18689200-18692400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr10:18689200-18692800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
49	chr10:18689400-18689800	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr10:18689400-18689800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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