Variant report

Variant	rs55822665
Chromosome Location	chr19:19383298-19383299
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19370401..19373352-chr19:19382111..19385169,3	K562	blood:
2	chr19:19371281..19373352-chr19:19383019..19385169,2	K562	blood:
3	chr19:19302936..19305152-chr19:19382979..19386540,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000187664	Chromatin interaction
ENSG00000064490	Chromatin interaction
ENSG00000254901	Chromatin interaction
ENSG00000064489	Chromatin interaction
ENSG00000213999	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10401714	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10403273	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10407933	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10422893	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10423874	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1064395	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11555053	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1557723	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17216041	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17751061	0.93[EUR][1000 genomes]
rs1989867	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2010506	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2011503	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2074302	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2315023	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2860494	0.81[AMR][1000 genomes]
rs2965190	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2965195	0.85[AMR][1000 genomes]
rs35854118	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4239639	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4808932	0.94[EUR][1000 genomes]
rs4808933	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4808934	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4808944	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55762233	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55765017	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56044734	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56135441	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56144632	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56212061	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56278919	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs57436187	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6511027	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6511029	0.83[AMR][1000 genomes]
rs7257875	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72999030	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72999059	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72999063	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72999068	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs756997	0.83[AMR][1000 genomes]
rs756999	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8100097	0.86[EUR][1000 genomes]
rs8108777	0.94[EUR][1000 genomes]
rs998732	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911303	chr19:19256870-19505087	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv911304	chr19:19303802-19408164	Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	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
4	nsv911306	chr19:19366643-19391838	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55822665	SF4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19373000-19384000	Weak transcription	Pancreas	Pancrea
2	chr19:19374000-19383400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr19:19374000-19383400	Weak transcription	Right Atrium	heart
4	chr19:19374200-19383600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr19:19381200-19383400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr19:19381600-19385600	Weak transcription	Brain Angular Gyrus	brain
7	chr19:19381600-19387600	Weak transcription	K562	blood
8	chr19:19382600-19383600	Flanking Active TSS	Fetal Intestine Large	intestine
9	chr19:19382800-19383600	Flanking Active TSS	Fetal Intestine Small	intestine
10	chr19:19383000-19383400	Flanking Active TSS	Duodenum Mucosa	Duodenum
11	chr19:19383000-19383400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
12	chr19:19383000-19383400	Flanking Active TSS	Stomach Mucosa	stomach
13	chr19:19383000-19383600	Bivalent Enhancer	Fetal Lung	lung
14	chr19:19383000-19383600	Enhancers	Placenta Amnion	Placenta Amnion
15	chr19:19383000-19383600	Flanking Active TSS	HepG2	liver
16	chr19:19383000-19383800	Flanking Active TSS	Liver	Liver
17	chr19:19383000-19384000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr19:19383000-19384200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
19	chr19:19383200-19383400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr19:19383200-19383400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr19:19383200-19383400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr19:19383200-19383400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr19:19383200-19383400	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
24	chr19:19383200-19383400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr19:19383200-19383400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
26	chr19:19383200-19383400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
27	chr19:19383200-19383400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr19:19383200-19383400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr19:19383200-19383400	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr19:19383200-19383400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr19:19383200-19383400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr19:19383200-19383400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr19:19383200-19383400	Bivalent/Poised TSS	Colonic Mucosa	Colon
34	chr19:19383200-19383400	Bivalent Enhancer	Fetal Muscle Leg	muscle
35	chr19:19383200-19383400	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
36	chr19:19383200-19383400	Flanking Active TSS	HSMMtube	muscle
37	chr19:19383200-19383400	Enhancers	NH-A	brain
38	chr19:19383200-19383600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
39	chr19:19383200-19383600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr19:19383200-19383600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr19:19383200-19383600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
42	chr19:19383200-19383600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
43	chr19:19383200-19383600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr19:19383200-19383800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr19:19383200-19384000	Active TSS	Rectal Mucosa Donor 29	rectum
46	chr19:19383200-19384200	Active TSS	Osteobl	bone
47	chr19:19383200-19384400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr19:19383200-19384400	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
49	chr19:19383200-19384600	Bivalent Enhancer	Fetal Brain Male	brain

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