Variant report

Variant	rs56291054
Chromosome Location	chr19:19509104-19509105
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:19495582..19499397-chr19:19505654..19509350,6	K562	blood:
2	chr19:19505389..19507306-chr19:19508971..19511086,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167491	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1036215	0.81[EUR][1000 genomes]
rs10406278	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11085264	0.86[EUR][1000 genomes]
rs11668203	0.94[EUR][1000 genomes]
rs11669558	0.82[EUR][1000 genomes]
rs11669730	0.83[EUR][1000 genomes]
rs11670687	0.86[EUR][1000 genomes]
rs11670761	0.83[EUR][1000 genomes]
rs11670775	0.83[EUR][1000 genomes]
rs11670882	0.81[EUR][1000 genomes]
rs11671253	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1529745	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1557723	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1560687	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16996127	0.84[EUR][1000 genomes]
rs17684164	0.84[EUR][1000 genomes]
rs1989867	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2011503	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2060274	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2060275	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2315023	0.82[AMR][1000 genomes]
rs2315282	0.83[EUR][1000 genomes]
rs2860494	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2905429	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2905433	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2905434	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2916070	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2916072	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2916075	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2965178	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2965179	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2965181	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2965184	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2965186	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2965187	0.87[AFR][1000 genomes]
rs2965190	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2965195	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2965201	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34487417	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34667451	0.86[EUR][1000 genomes]
rs4239639	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs45556231	0.83[EUR][1000 genomes]
rs45631651	0.83[EUR][1000 genomes]
rs4808204	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4808205	0.83[EUR][1000 genomes]
rs4808206	0.83[EUR][1000 genomes]
rs4808944	0.82[AMR][1000 genomes]
rs4808951	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4808958	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4808962	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4808968	0.83[EUR][1000 genomes]
rs4808969	0.83[EUR][1000 genomes]
rs4808970	0.82[EUR][1000 genomes]
rs55927782	0.83[EUR][1000 genomes]
rs56280531	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56330647	0.84[EUR][1000 genomes]
rs57436187	0.86[AMR][1000 genomes]
rs58074958	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61744761	0.82[EUR][1000 genomes]
rs6511029	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7245689	0.84[EUR][1000 genomes]
rs7250233	0.84[EUR][1000 genomes]
rs7252453	0.82[EUR][1000 genomes]
rs7256028	0.84[EUR][1000 genomes]
rs751857	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs754256	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs756997	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs756999	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8100927	0.83[EUR][1000 genomes]
rs8101219	0.83[EUR][1000 genomes]
rs8102502	0.80[EUR][1000 genomes]
rs8105642	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8110171	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8110250	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8111093	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv1056419	chr19:19421218-19510611	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56291054	SF4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19497600-19515800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:19498000-19510400	Weak transcription	A549	lung
3	chr19:19498000-19510400	Weak transcription	NHDF-Ad	bronchial
4	chr19:19498000-19515600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr19:19498200-19510400	Weak transcription	Fetal Stomach	stomach
6	chr19:19498400-19513600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr19:19499800-19510400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:19500200-19510400	Weak transcription	Brain Hippocampus Middle	brain
9	chr19:19500400-19509800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr19:19500400-19515400	Weak transcription	Fetal Heart	heart
11	chr19:19500600-19510400	Weak transcription	Fetal Kidney	kidney
12	chr19:19500600-19515800	Weak transcription	Right Ventricle	heart
13	chr19:19501200-19514000	Weak transcription	Pancreas	Pancrea
14	chr19:19501400-19511000	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr19:19501400-19513600	Weak transcription	Psoas Muscle	Psoas
16	chr19:19501400-19513800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr19:19501800-19510800	Weak transcription	Brain Substantia Nigra	brain
18	chr19:19502600-19510400	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr19:19504600-19510400	Weak transcription	Fetal Lung	lung
20	chr19:19505600-19514200	Weak transcription	Small Intestine	intestine
21	chr19:19505800-19510000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr19:19505800-19513800	Weak transcription	Stomach Mucosa	stomach
23	chr19:19506000-19509800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr19:19506000-19510000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr19:19506000-19510000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr19:19506000-19510200	Weak transcription	NHLF	lung
27	chr19:19506000-19510400	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr19:19506000-19510400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr19:19506000-19510600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr19:19506000-19510600	Weak transcription	Fetal Muscle Leg	muscle
31	chr19:19506000-19510600	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr19:19506000-19510600	Weak transcription	Thymus	Thymus
33	chr19:19506000-19510800	Weak transcription	HMEC	breast
34	chr19:19506000-19511000	Weak transcription	Fetal Muscle Trunk	muscle
35	chr19:19506000-19511000	Weak transcription	Right Atrium	heart
36	chr19:19506000-19512800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr19:19506000-19513600	Weak transcription	Hela-S3	cervix
38	chr19:19506000-19513600	Weak transcription	HepG2	liver
39	chr19:19506000-19513800	Weak transcription	Primary B cells from cord blood	blood
40	chr19:19506000-19513800	Weak transcription	Fetal Intestine Large	intestine
41	chr19:19506000-19514000	Weak transcription	Esophagus	oesophagus
42	chr19:19506000-19515600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr19:19506000-19515800	Weak transcription	Colonic Mucosa	Colon
44	chr19:19506000-19515800	Weak transcription	Left Ventricle	heart
45	chr19:19506200-19510200	Weak transcription	HUVEC	blood vessel
46	chr19:19506200-19510400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr19:19506200-19510400	Weak transcription	Brain Anterior Caudate	brain
48	chr19:19506200-19510600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr19:19506200-19510600	Weak transcription	Liver	Liver
50	chr19:19506200-19510600	Weak transcription	HSMMtube	muscle

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