Variant report

Variant	rs4808958
Chromosome Location	chr19:19571752-19571753
allele	A/G
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	POLR2A	chr19:19571483-19571929	GM12892	blood:	n/a	n/a
2	POU2F2	chr19:19571300-19571845	GM12891	blood:	n/a	n/a
3	BCLAF1	chr19:19571489-19571914	GM12878	blood:	n/a	n/a
4	MYC	chr19:19571592-19571847	K562	blood:	n/a	chr19:19571679-19571690
5	ELF1	chr19:19570525-19572008	GM12878	blood:	n/a	chr19:19570797-19570810
6	E2F6	chr19:19571568-19572222	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr19:19570975-19571987	GM12878	blood:	n/a	n/a
8	MXI1	chr19:19571103-19572039	IMR90	lung:	n/a	n/a
9	SIN3A	chr19:19571577-19571820	H1-hESC	embryonic stem cell:	n/a	n/a
10	E2F6	chr19:19571626-19571894	K562	blood:	n/a	n/a
11	POLR2A	chr19:19571558-19571908	GM12891	blood:	n/a	n/a
12	POLR2A	chr19:19571495-19571767	GM12892	blood:	n/a	n/a
13	MYC	chr19:19571520-19571933	HUVEC	blood vessel:	n/a	chr19:19571679-19571690
14	MAX	chr19:19571530-19571908	GM12878	blood:	n/a	chr19:19571679-19571690
15	CHD2	chr19:19571546-19571924	GM12878	blood:	n/a	n/a
16	POLR2A	chr19:19570714-19571830	GM15510	blood:	n/a	n/a
17	POLR2A	chr19:19570398-19571981	GM12878	blood:	n/a	n/a
18	ELF1	chr19:19571581-19571830	K562	blood:	n/a	n/a
19	POLR2A	chr19:19570429-19571997	HL-60	blood:	n/a	n/a
20	POLR2A	chr19:19571471-19571963	GM12878	blood:	n/a	n/a
21	MAX	chr19:19571460-19571957	H1-hESC	embryonic stem cell:	n/a	chr19:19571679-19571690
22	POLR2A	chr19:19570533-19571967	GM12891	blood:	n/a	n/a
23	POLR2A	chr19:19571476-19572131	GM12892	blood:	n/a	n/a
24	POLR2A	chr19:19571462-19572079	GM12892	blood:	n/a	n/a
25	POLR2A	chr19:19571562-19571874	K562	blood:	n/a	n/a
26	MXI1	chr19:19571495-19571904	GM12878	blood:	n/a	n/a
27	POLR2A	chr19:19571373-19572010	GM12891	blood:	n/a	n/a
28	ELF1	chr19:19571529-19571972	GM12878	blood:	n/a	n/a
29	POLR2A	chr19:19570908-19572076	GM12891	blood:	n/a	n/a
30	POLR2A	chr19:19571651-19571755	HUVEC	blood vessel:	n/a	n/a
31	ZNF263	chr19:19571278-19573525	HEK293-T-REx	kidney:	n/a	chr19:19572602-19572623 chr19:19572607-19572616 chr19:19573057-19573066
32	POLR2A	chr19:19571457-19572021	GM12891	blood:	n/a	n/a
33	MYC	chr19:19571732-19571821	MCF-7	breast:	n/a	n/a
34	MAX	chr19:19571443-19572070	H1-hESC	embryonic stem cell:	n/a	chr19:19571679-19571690
35	MAZ	chr19:19571592-19571877	GM12878	blood:	n/a	chr19:19571679-19571690
36	MTA3	chr19:19570204-19572179	GM12878	blood:	n/a	n/a
37	POLR2A	chr19:19570587-19571916	GM18505	blood:	n/a	n/a
38	ELF1	chr19:19571552-19571881	K562	blood:	n/a	n/a
39	ELK1	chr19:19571646-19571831	GM12878	blood:	n/a	n/a
40	MYC	chr19:19571620-19571850	K562	blood:	n/a	chr19:19571679-19571690
41	POLR2A	chr19:19570948-19571987	K562	blood:	n/a	n/a
42	MAX	chr19:19571505-19571979	K562	blood:	n/a	chr19:19571679-19571690
43	STAT1	chr19:19571743-19571859	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:19570132..19572642-chr19:19597884..19599709,3	K562	blood:
2	chr19:19515386..19519519-chr19:19571187..19573375,3	K562	blood:
3	chr19:19495597..19498246-chr19:19571107..19572849,2	K562	blood:
4	chr19:19571238..19573571-chr19:19586807..19589450,2	MCF-7	breast:
5	chr19:19569495..19572698-chr19:19572718..19574339,3	K562	blood:
6	chr19:19570376..19575066-chr19:19577857..19582377,6	K562	blood:
7	chr19:19569916..19571942-chr19:19620244..19622039,2	K562	blood:
8	chr19:19571714..19574433-chr19:19574654..19576215,2	K562	blood:
9	chr19:19520647..19523347-chr19:19569351..19571784,4	K562	blood:

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

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10406278	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11085264	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11668203	0.94[EUR][1000 genomes]
rs11669558	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11669730	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11670687	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11670761	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11670775	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11670882	0.81[EUR][1000 genomes]
rs11671253	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1529745	0.84[EUR][1000 genomes]
rs1560687	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16996127	0.84[EUR][1000 genomes]
rs17684164	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2060274	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2060275	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2905429	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2905433	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2905434	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2916070	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2916072	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2916075	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2965179	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2965181	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2965184	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2965186	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2965187	0.84[AFR][1000 genomes]
rs2965201	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs34487417	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34667451	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs45556231	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs45631651	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4808204	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4808205	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4808206	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4808951	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4808962	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4808968	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4808969	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4808970	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55927782	0.83[EUR][1000 genomes]
rs56280531	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56291054	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56330647	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs58074958	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61744761	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7245689	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7250233	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7252453	0.81[EUR][1000 genomes]
rs7256028	0.84[EUR][1000 genomes]
rs751857	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs754256	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8100927	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8101219	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8105642	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8110171	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8110250	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8111093	0.90[AFR][1000 genomes];0.85[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
rs4808958	SF4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19564400-19571800	Weak transcription	Fetal Kidney	kidney
2	chr19:19567000-19573600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr19:19567000-19575000	Enhancers	Spleen	Spleen
4	chr19:19567000-19576200	Enhancers	Gastric	stomach
5	chr19:19567000-19576600	Genic enhancers	Fetal Intestine Small	intestine
6	chr19:19567200-19576000	Enhancers	Fetal Intestine Large	intestine
7	chr19:19567400-19575000	Enhancers	Small Intestine	intestine
8	chr19:19568200-19575600	Enhancers	Lung	lung
9	chr19:19568200-19575800	Enhancers	Placenta	Placenta
10	chr19:19568400-19575400	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr19:19568600-19572600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr19:19568600-19575400	Enhancers	Liver	Liver
13	chr19:19568600-19575400	Enhancers	Psoas Muscle	Psoas
14	chr19:19568600-19575600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr19:19568600-19575800	Enhancers	Left Ventricle	heart
16	chr19:19568600-19575800	Enhancers	Right Atrium	heart
17	chr19:19568600-19576000	Enhancers	Fetal Lung	lung
18	chr19:19568600-19576200	Enhancers	Stomach Mucosa	stomach
19	chr19:19568600-19576400	Enhancers	Pancreas	Pancrea
20	chr19:19568800-19574800	Enhancers	HSMMtube	muscle
21	chr19:19568800-19575000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
22	chr19:19568800-19575000	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr19:19569000-19572400	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr19:19569000-19575400	Enhancers	Right Ventricle	heart
25	chr19:19569000-19575800	Enhancers	Esophagus	oesophagus
26	chr19:19569200-19572000	Flanking Active TSS	GM12878-XiMat	blood
27	chr19:19569200-19575600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr19:19569200-19575800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr19:19569200-19576200	Weak transcription	Hela-S3	cervix
30	chr19:19569400-19571800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr19:19569400-19572400	Flanking Active TSS	Primary B cells from cord blood	blood
32	chr19:19569400-19572600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr19:19569400-19572800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
34	chr19:19569400-19573800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr19:19569400-19575800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr19:19569600-19572400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
37	chr19:19569600-19572400	Enhancers	Fetal Muscle Trunk	muscle
38	chr19:19569600-19572600	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr19:19569600-19572600	Flanking Active TSS	Primary T cells from cord blood	blood
40	chr19:19569600-19572800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr19:19569600-19573200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr19:19569600-19575400	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr19:19569600-19575600	Enhancers	Brain Substantia Nigra	brain
44	chr19:19569800-19571800	Weak transcription	HepG2	liver
45	chr19:19569800-19572200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
46	chr19:19569800-19572400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
47	chr19:19569800-19572600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr19:19569800-19572600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
49	chr19:19569800-19572600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr19:19569800-19572600	Enhancers	Fetal Muscle Leg	muscle

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