Variant report

Variant	rs56353321
Chromosome Location	chr19:44592403-44592404
allele	C/T
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	chr19:44590880-44594869	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:44590412..44592752-chr19:44596978..44598505,2	K562	blood:
2	chr19:44589107..44593140-chr19:44596665..44599244,3	MCF-7	breast:

Variant related genes	Relation type
RNU6-902P	TF binding region
RN7SL53P	TF binding region
ENSG00000267680	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10410306	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10420143	0.94[ASN][1000 genomes]
rs10853771	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2061332	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2061333	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2284981	0.80[EUR][1000 genomes]
rs28446946	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs28539456	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3172	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3200505	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3746319	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3746321	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4429390	0.86[EUR][1000 genomes]
rs4459653	0.86[EUR][1000 genomes]
rs4508518	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4802204	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4802205	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4802206	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4802207	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4803681	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55876899	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62115524	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62115526	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7250004	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7250005	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7508149	0.90[ASN][1000 genomes]
rs8099869	0.81[AMR][1000 genomes]
rs8104573	0.94[ASN][1000 genomes]
rs8105860	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs8108021	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8108404	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs8113249	0.81[EUR][1000 genomes]
rs8113750	0.92[ASN][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	nsv833840	chr19:44520620-44715760	Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56353321	ZNF224	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44577000-44598000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:44577200-44598000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr19:44577600-44597800	Weak transcription	HMEC	breast
4	chr19:44580600-44592600	Strong transcription	Duodenum Smooth Muscle	Duodenum
5	chr19:44580800-44593200	Strong transcription	Cortex derived primary cultured neurospheres	brain
6	chr19:44581200-44593000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr19:44581800-44592800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr19:44582000-44592600	Strong transcription	Fetal Stomach	stomach
9	chr19:44582200-44592800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr19:44583200-44593000	Strong transcription	Fetal Brain Female	brain
11	chr19:44583600-44593200	Strong transcription	Skeletal Muscle Male	skeletal muscle
12	chr19:44584000-44592800	ZNF genes & repeats	Liver	Liver
13	chr19:44584000-44593400	Strong transcription	Adipose Nuclei	Adipose
14	chr19:44584200-44592800	Strong transcription	Left Ventricle	heart
15	chr19:44584200-44593400	Strong transcription	Fetal Lung	lung
16	chr19:44584200-44593400	Strong transcription	Ovary	ovary
17	chr19:44584800-44592800	Strong transcription	Fetal Muscle Leg	muscle
18	chr19:44586800-44598000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr19:44587000-44597800	Weak transcription	HUVEC	blood vessel
20	chr19:44587000-44598000	Weak transcription	Fetal Thymus	thymus
21	chr19:44587200-44597800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr19:44588400-44593400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
23	chr19:44588400-44597600	Weak transcription	HepG2	liver
24	chr19:44588600-44597800	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr19:44588600-44597800	Weak transcription	GM12878-XiMat	blood
26	chr19:44589200-44598000	Weak transcription	Colonic Mucosa	Colon
27	chr19:44589400-44598000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr19:44589400-44598200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr19:44589600-44598000	Weak transcription	Right Ventricle	heart
30	chr19:44590000-44598200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr19:44590200-44597800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr19:44590200-44598200	Weak transcription	Esophagus	oesophagus
33	chr19:44590400-44598000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr19:44590400-44598000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr19:44590400-44598000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr19:44590400-44598000	Weak transcription	NHEK	skin
37	chr19:44590600-44593000	Weak transcription	A549	lung
38	chr19:44590600-44598000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr19:44590600-44598000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr19:44590600-44598000	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr19:44590600-44598000	Weak transcription	Placenta	Placenta
42	chr19:44590800-44597800	Weak transcription	NHLF	lung
43	chr19:44590800-44598000	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr19:44590800-44598000	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr19:44590800-44598000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr19:44590800-44598000	Weak transcription	Colon Smooth Muscle	Colon
47	chr19:44590800-44598000	Weak transcription	Fetal Brain Male	brain
48	chr19:44590800-44598200	Weak transcription	Gastric	stomach
49	chr19:44591000-44593200	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr19:44591000-44597800	Weak transcription	HUES48 Cell Line	embryonic stem cell

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