Variant report

Variant	rs55927782
Chromosome Location	chr19:19642032-19642033
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19624801..19628442-chr19:19640614..19645032,4	MCF-7	breast:
2	chr19:19637478..19643205-chr19:19752988..19755970,5	MCF-7	breast:
3	chr19:19640933..19643322-chr19:19754453..19756328,2	K562	blood:
4	chr19:19625745..19628806-chr19:19639215..19643547,5	K562	blood:
5	chr19:19640161..19645536-chr19:19752406..19756434,6	K562	blood:
6	chr19:19641380..19649124-chr19:19737025..19742358,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000089639	Chromatin interaction
ENSG00000178093	Chromatin interaction
ENSG00000064547	Chromatin interaction
ENSG00000186010	Chromatin interaction
ENSG00000258674	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1036215	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10406278	0.82[EUR][1000 genomes]
rs11085264	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11668203	0.89[EUR][1000 genomes]
rs11669558	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11669730	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11670687	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11670761	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11670775	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11670882	0.95[EUR][1000 genomes]
rs11671253	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1560687	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16996127	0.99[EUR][1000 genomes]
rs17684164	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2060274	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2060275	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2905434	0.81[EUR][1000 genomes]
rs2916070	0.85[EUR][1000 genomes]
rs2916072	0.89[EUR][1000 genomes]
rs2916075	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2965179	0.85[EUR][1000 genomes]
rs2965181	0.85[EUR][1000 genomes]
rs2965184	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2965186	0.81[EUR][1000 genomes]
rs34487417	0.83[EUR][1000 genomes]
rs34667451	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs45556231	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45631651	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4808204	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4808205	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4808206	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4808951	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4808958	0.83[EUR][1000 genomes]
rs4808962	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4808968	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4808969	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4808970	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56280531	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56291054	0.83[EUR][1000 genomes]
rs56330647	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58074958	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61744761	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7245689	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7250233	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7252453	0.96[EUR][1000 genomes]
rs7256028	0.99[EUR][1000 genomes]
rs751857	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs754256	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8100927	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8101219	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8102502	0.94[EUR][1000 genomes]
rs8105642	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8110171	0.88[EUR][1000 genomes]
rs8110250	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8111093	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv911307	chr19:19631655-19657143	Bivalent Enhancer Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv911308	chr19:19631655-19663850	Strong transcription Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	esv1807343	chr19:19639345-19669570	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55927782	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	chr19:19628200-19642800	Weak transcription	Stomach Mucosa	stomach
2	chr19:19628200-19643000	Weak transcription	HUVEC	blood vessel
3	chr19:19628400-19642800	Weak transcription	Hela-S3	cervix
4	chr19:19629000-19643600	Weak transcription	Small Intestine	intestine
5	chr19:19630400-19643000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr19:19630600-19642800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr19:19630600-19651800	Weak transcription	A549	lung
8	chr19:19630800-19642800	Weak transcription	NHEK	skin
9	chr19:19630800-19643000	Weak transcription	NHDF-Ad	bronchial
10	chr19:19631000-19647800	Weak transcription	HSMMtube	muscle
11	chr19:19634000-19643000	Strong transcription	Fetal Intestine Small	intestine
12	chr19:19634400-19643000	Weak transcription	K562	blood
13	chr19:19635200-19649200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr19:19636000-19642400	Strong transcription	Primary T cells from cord blood	blood
15	chr19:19636800-19643000	Weak transcription	Right Atrium	heart
16	chr19:19637800-19644400	Weak transcription	Fetal Heart	heart
17	chr19:19638400-19642200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr19:19638400-19643000	Weak transcription	NH-A	brain
19	chr19:19638400-19648800	Weak transcription	GM12878-XiMat	blood
20	chr19:19638600-19642400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr19:19638800-19643000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr19:19639000-19648600	Weak transcription	Aorta	Aorta
23	chr19:19639200-19643400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr19:19639200-19643400	Weak transcription	HepG2	liver
25	chr19:19639200-19648000	Weak transcription	Ovary	ovary
26	chr19:19639400-19642800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr19:19639400-19642800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr19:19639400-19642800	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr19:19639400-19642800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr19:19639400-19643000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr19:19639400-19643000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr19:19639400-19643000	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr19:19639400-19643000	Weak transcription	Pancreas	Pancrea
34	chr19:19639400-19643400	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr19:19639400-19644800	Weak transcription	Fetal Intestine Large	intestine
36	chr19:19639400-19648200	Weak transcription	Primary B cells from cord blood	blood
37	chr19:19639600-19643000	Weak transcription	Esophagus	oesophagus
38	chr19:19639600-19643000	Weak transcription	Placenta	Placenta
39	chr19:19639600-19643400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr19:19639600-19648600	Weak transcription	NHLF	lung
41	chr19:19639800-19643000	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr19:19640000-19642600	Strong transcription	Fetal Stomach	stomach
43	chr19:19640000-19642600	Strong transcription	Right Ventricle	heart
44	chr19:19640000-19642800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr19:19640000-19643000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr19:19640000-19643000	Weak transcription	Brain Substantia Nigra	brain
47	chr19:19640000-19643000	Weak transcription	Rectal Smooth Muscle	rectum
48	chr19:19640200-19642800	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr19:19640200-19643000	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr19:19640200-19643000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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