Variant report

Variant	rs58074958
Chromosome Location	chr19:19570555-19570556
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:39)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:39 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr19:19570500-19570650	GM12873	blood:	n/a	n/a
2	POLR2A	chr19:19570370-19571464	GM12892	blood:	n/a	n/a
3	POLR2A	chr19:19570504-19571007	HUVEC	blood vessel:	n/a	n/a
4	ELF1	chr19:19570525-19572008	GM12878	blood:	n/a	chr19:19570797-19570810
5	GABPA	chr19:19570356-19571085	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr19:19570508-19570856	SK-N-SH	brain:	n/a	n/a
7	MYC	chr19:19570529-19570630	K562	blood:	n/a	n/a
8	ELF1	chr19:19570457-19571006	GM12878	blood:	n/a	chr19:19570797-19570810
9	RUNX3	chr19:19570373-19570964	GM12878	blood:	n/a	n/a
10	SIN3AK20	chr19:19570531-19570989	SK-N-SH	brain:	n/a	n/a
11	PBX3	chr19:19570278-19571073	SK-N-SH	brain:	n/a	chr19:19570550-19570559
12	POLR2A	chr19:19570398-19571981	GM12878	blood:	n/a	n/a
13	POLR2A	chr19:19570465-19571391	GM12892	blood:	n/a	n/a
14	POLR2A	chr19:19570429-19571997	HL-60	blood:	n/a	n/a
15	POLR2A	chr19:19570452-19571384	PFSK-1	brain:	n/a	n/a
16	RCOR1	chr19:19570496-19570761	K562	blood:	n/a	n/a
17	POLR2A	chr19:19570533-19571967	GM12891	blood:	n/a	n/a
18	ZNF384	chr19:19569979-19570596	GM12878	blood:	n/a	n/a
19	PBX3	chr19:19570260-19571022	SK-N-SH	brain:	n/a	chr19:19570550-19570559
20	POLR2A	chr19:19570496-19571194	K562	blood:	n/a	n/a
21	POLR2A	chr19:19570416-19570886	K562	blood:	n/a	n/a
22	POLR2A	chr19:19570480-19570692	GM12878	blood:	n/a	n/a
23	POLR2A	chr19:19570460-19571362	GM12891	blood:	n/a	n/a
24	ELK1	chr19:19570538-19570977	GM12878	blood:	n/a	n/a
25	SIN3AK20	chr19:19570505-19570822	PFSK-1	brain:	n/a	n/a
26	POLR2A	chr19:19570317-19571343	HUVEC	blood vessel:	n/a	n/a
27	POLR2A	chr19:19570537-19570919	GM12891	blood:	n/a	n/a
28	POLR2A	chr19:19570319-19571117	U87	brain:	n/a	n/a
29	FOS	chr19:19570006-19571389	HUVEC	blood vessel:	n/a	n/a
30	STAT5A	chr19:19570344-19571019	GM12878	blood:	n/a	n/a
31	MTA3	chr19:19570204-19572179	GM12878	blood:	n/a	n/a
32	RFX5	chr19:19570485-19570825	GM12878	blood:	n/a	n/a
33	BRCA1	chr19:19570478-19570586	GM12878	blood:	n/a	n/a
34	RUNX3	chr19:19570117-19570921	GM12878	blood:	n/a	n/a
35	POLR2A	chr19:19570545-19570561	K562	blood:	n/a	n/a
36	PBX3	chr19:19570478-19570659	GM12878	blood:	n/a	chr19:19570550-19570559
37	EP300	chr19:19570506-19570857	SK-N-SH_RA	brain:	n/a	n/a
38	MTA3	chr19:19570345-19570945	GM12878	blood:	n/a	n/a
39	POLR2A	chr19:19570428-19571117	U87	brain:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19570132..19572642-chr19:19597884..19599709,3	K562	blood:
2	chr19:19524964..19526916-chr19:19569433..19571112,2	MCF-7	breast:
3	chr19:19515119..19517741-chr19:19568755..19571176,2	MCF-7	breast:
4	chr19:19569495..19572698-chr19:19572718..19574339,3	K562	blood:
5	chr19:19570376..19575066-chr19:19577857..19582377,6	K562	blood:
6	chr19:19569916..19571942-chr19:19620244..19622039,2	K562	blood:
7	chr19:19520647..19523347-chr19:19569351..19571784,4	K562	blood:

No data

Variant related genes	Relation type
GATAD2A	TF binding region
ENSG00000167491	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1036215	0.85[EUR][1000 genomes]
rs10406278	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs11085264	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11668203	1.00[EUR][1000 genomes]
rs11669558	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11669730	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11670687	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11670761	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11670775	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11670882	0.86[EUR][1000 genomes]
rs11671253	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1529745	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1560687	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16996127	0.90[EUR][1000 genomes]
rs17684164	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2060274	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2060275	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2860494	0.82[EUR][1000 genomes]
rs2905429	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2905433	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2905434	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2916070	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2916072	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2916075	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2965178	0.83[EUR][1000 genomes]
rs2965179	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2965181	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2965184	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2965186	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2965187	0.85[AFR][1000 genomes]
rs2965195	0.83[EUR][1000 genomes]
rs2965201	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs34487417	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34667451	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs45556231	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs45631651	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4808204	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4808205	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4808206	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4808951	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4808958	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4808962	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4808968	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4808969	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4808970	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55927782	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56280531	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56291054	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56330647	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61744761	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6511029	0.81[EUR][1000 genomes]
rs7245689	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7250233	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7252453	0.87[EUR][1000 genomes]
rs7256028	0.90[EUR][1000 genomes]
rs751857	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs754256	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs756997	0.83[EUR][1000 genomes]
rs8100927	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8101219	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8102502	0.86[EUR][1000 genomes]
rs8105642	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8110171	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8110250	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8111093	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][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	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs58074958	SF4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19545800-19570600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr19:19551000-19571200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:19558200-19571400	Weak transcription	Brain Germinal Matrix	brain
4	chr19:19559200-19570600	Weak transcription	Fetal Brain Female	brain
5	chr19:19561400-19570600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr19:19563400-19570600	Weak transcription	A549	lung
7	chr19:19564400-19571800	Weak transcription	Fetal Kidney	kidney
8	chr19:19567000-19573600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr19:19567000-19575000	Enhancers	Spleen	Spleen
10	chr19:19567000-19576200	Enhancers	Gastric	stomach
11	chr19:19567000-19576600	Genic enhancers	Fetal Intestine Small	intestine
12	chr19:19567200-19576000	Enhancers	Fetal Intestine Large	intestine
13	chr19:19567400-19575000	Enhancers	Small Intestine	intestine
14	chr19:19567800-19571200	Genic enhancers	Dnd41	blood
15	chr19:19568000-19570800	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr19:19568200-19571600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr19:19568200-19575600	Enhancers	Lung	lung
18	chr19:19568200-19575800	Enhancers	Placenta	Placenta
19	chr19:19568400-19575400	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr19:19568600-19570600	Genic enhancers	HSMM	muscle
21	chr19:19568600-19570800	Enhancers	Adipose Nuclei	Adipose
22	chr19:19568600-19571000	Enhancers	Fetal Stomach	stomach
23	chr19:19568600-19571600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr19:19568600-19572600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr19:19568600-19575400	Enhancers	Liver	Liver
26	chr19:19568600-19575400	Enhancers	Psoas Muscle	Psoas
27	chr19:19568600-19575600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr19:19568600-19575800	Enhancers	Left Ventricle	heart
29	chr19:19568600-19575800	Enhancers	Right Atrium	heart
30	chr19:19568600-19576000	Enhancers	Fetal Lung	lung
31	chr19:19568600-19576200	Enhancers	Stomach Mucosa	stomach
32	chr19:19568600-19576400	Enhancers	Pancreas	Pancrea
33	chr19:19568800-19571600	Enhancers	Brain Anterior Caudate	brain
34	chr19:19568800-19574800	Enhancers	HSMMtube	muscle
35	chr19:19568800-19575000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
36	chr19:19568800-19575000	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr19:19569000-19570600	Enhancers	Thymus	Thymus
38	chr19:19569000-19570800	Enhancers	Fetal Thymus	thymus
39	chr19:19569000-19572400	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr19:19569000-19575400	Enhancers	Right Ventricle	heart
41	chr19:19569000-19575800	Enhancers	Esophagus	oesophagus
42	chr19:19569200-19572000	Flanking Active TSS	GM12878-XiMat	blood
43	chr19:19569200-19575600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr19:19569200-19575800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr19:19569200-19576200	Weak transcription	Hela-S3	cervix
46	chr19:19569400-19570800	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr19:19569400-19571400	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr19:19569400-19571400	Genic enhancers	NHEK	skin
49	chr19:19569400-19571800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr19:19569400-19572400	Flanking Active TSS	Primary B cells from cord blood	blood

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