Variant report

Variant	rs56280531
Chromosome Location	chr19:19585788-19585789
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19585265..19586941-chr19:19595062..19597219,2	K562	blood:
2	chr19:19584133..19587197-chr19:19592002..19595372,3	K562	blood:
3	chr19:19577936..19580342-chr19:19585609..19587741,3	MCF-7	breast:
4	chr19:19584315..19588308-chr19:19588802..19591974,4	K562	blood:
5	chr19:19580831..19583054-chr19:19584529..19587065,3	K562	blood:
6	chr19:19581501..19584310-chr19:19584529..19586340,3	K562	blood:
7	chr19:19585281..19589285-chr19:19590381..19594944,7	K562	blood:
8	chr19:19496791..19501491-chr19:19584169..19587621,5	MCF-7	breast:
9	chr19:19574214..19577811-chr19:19584018..19587977,5	MCF-7	breast:
10	chr19:19579004..19580878-chr19:19585404..19588085,2	MCF-7	breast:

No data

Variant related genes	Relation type
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]
rs1036215	0.93[EUR][1000 genomes]
rs10406278	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11085264	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11668203	0.92[EUR][1000 genomes]
rs11669558	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11669730	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11670687	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11670761	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11670775	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11670882	0.94[EUR][1000 genomes]
rs11671253	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1529745	0.83[EUR][1000 genomes]
rs1560687	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16996127	0.98[EUR][1000 genomes]
rs17684164	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2060274	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2060275	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2905429	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2905434	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2916070	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2916072	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2916075	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2965179	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2965181	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2965184	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2965186	0.84[EUR][1000 genomes]
rs2965201	0.81[AFR][1000 genomes]
rs34487417	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34667451	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45556231	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs45631651	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4808204	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4808205	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4808206	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4808951	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4808958	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4808962	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4808968	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4808969	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4808970	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55927782	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56291054	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56330647	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58074958	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61744761	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7245689	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7250233	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7252453	0.95[EUR][1000 genomes]
rs7256028	0.98[EUR][1000 genomes]
rs751857	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs754256	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8100927	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8101219	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8102502	0.93[EUR][1000 genomes]
rs8105642	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8110171	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8110250	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8111093	0.84[AFR][1000 genomes];0.83[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
rs56280531	SF4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19577800-19598000	Weak transcription	Ovary	ovary
2	chr19:19579200-19585800	Weak transcription	Hela-S3	cervix
3	chr19:19579200-19586000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr19:19579200-19598000	Weak transcription	Small Intestine	intestine
5	chr19:19579400-19599400	Weak transcription	Brain Angular Gyrus	brain
6	chr19:19579800-19587400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr19:19579800-19591000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr19:19579800-19593400	Weak transcription	Fetal Kidney	kidney
9	chr19:19579800-19595600	Weak transcription	Osteobl	bone
10	chr19:19579800-19595800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr19:19579800-19595800	Weak transcription	Colon Smooth Muscle	Colon
12	chr19:19579800-19595800	Weak transcription	HUVEC	blood vessel
13	chr19:19579800-19598600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr19:19579800-19599200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr19:19579800-19599800	Weak transcription	Brain Substantia Nigra	brain
16	chr19:19580600-19595200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr19:19580600-19597200	Weak transcription	Brain Anterior Caudate	brain
18	chr19:19580800-19593600	Strong transcription	Fetal Intestine Small	intestine
19	chr19:19581400-19589000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr19:19581600-19585800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr19:19581600-19587800	Strong transcription	NHEK	skin
22	chr19:19581600-19595200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr19:19581800-19587000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr19:19582200-19597600	Strong transcription	Dnd41	blood
25	chr19:19582600-19586800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr19:19583200-19586400	Weak transcription	Stomach Mucosa	stomach
27	chr19:19583200-19587400	Strong transcription	Primary B cells from cord blood	blood
28	chr19:19583400-19585800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr19:19583400-19586000	Strong transcription	Stomach Smooth Muscle	stomach
30	chr19:19583400-19586200	Strong transcription	Gastric	stomach
31	chr19:19583400-19587600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr19:19583400-19588000	Genic enhancers	Spleen	Spleen
33	chr19:19583400-19588400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr19:19583400-19588800	Genic enhancers	Primary T cells fromperipheralblood	blood
35	chr19:19583600-19585800	Strong transcription	Fetal Stomach	stomach
36	chr19:19583600-19586000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
37	chr19:19583600-19586000	Genic enhancers	HSMM	muscle
38	chr19:19583600-19586200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr19:19583600-19586200	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr19:19583600-19586400	Genic enhancers	Fetal Muscle Leg	muscle
41	chr19:19583600-19587000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
42	chr19:19583600-19587200	Strong transcription	Liver	Liver
43	chr19:19583600-19588000	Genic enhancers	K562	blood
44	chr19:19583600-19588200	Strong transcription	Fetal Intestine Large	intestine
45	chr19:19583600-19588600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr19:19583600-19588800	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr19:19583600-19589200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr19:19583600-19593200	Weak transcription	Fetal Lung	lung
49	chr19:19583800-19585800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr19:19583800-19586000	Genic enhancers	Fetal Muscle Trunk	muscle

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