Variant report

Variant	rs6553396
Chromosome Location	chr4:190864015-190864016
allele	A/C
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	ZBTB33	chr4:190863382-190864055	HepG2	liver:	n/a	n/a
2	SPI1	chr4:190863823-190864033	GM12878	blood:	n/a	n/a
3	EBF1	chr4:190863519-190864055	GM12878	blood:	n/a	n/a
4	EBF1	chr4:190863707-190864052	GM12878	blood:	n/a	n/a
5	SP1	chr4:190863349-190864252	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ENSG00000245685	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10001956	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11132770	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11132771	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1138718	0.80[EUR][1000 genomes]
rs11736363	0.80[AMR][1000 genomes]
rs11736387	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11736960	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12646565	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12646667	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12646672	0.91[EUR][1000 genomes]
rs12649488	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12649515	0.91[EUR][1000 genomes]
rs13121836	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13121986	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13131647	0.81[EUR][1000 genomes]
rs13133725	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13133958	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13140896	0.85[AFR][1000 genomes]
rs13146111	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13148101	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1961818	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2037947	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2037948	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2078634	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2293865	0.81[ASN][1000 genomes]
rs2411530	0.82[EUR][1000 genomes]
rs2411549	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2411550	0.81[ASN][1000 genomes]
rs3775989	0.87[EUR][1000 genomes]
rs4145515	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4145516	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4145517	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60965499	0.80[EUR][1000 genomes]
rs6816856	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6820684	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6837422	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7657916	0.98[EUR][1000 genomes]
rs7658339	0.97[EUR][1000 genomes]
rs7668489	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7675870	0.89[EUR][1000 genomes]
rs7691161	0.93[EUR][1000 genomes]
rs9990612	0.81[EUR][1000 genomes]
rs9992042	0.94[EUR][1000 genomes]
rs9996679	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6553396	AF146191.4	cis	Esophagus Muscularis	GTEx
rs6553396	AF146191.4	cis	Thyroid	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:190858600-190865400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
2	chr4:190860600-190864200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
3	chr4:190861600-190864200	Active TSS	Aorta	Aorta
4	chr4:190861600-190864200	Active TSS	GM12878-XiMat	blood
5	chr4:190862600-190868800	Weak transcription	Lung	lung
6	chr4:190862600-190868800	Weak transcription	Pancreas	Pancrea
7	chr4:190862600-190869800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr4:190862600-190881000	Weak transcription	Spleen	Spleen
9	chr4:190862800-190864200	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr4:190862800-190865200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr4:190862800-190867000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr4:190863000-190864200	Enhancers	Brain Cingulate Gyrus	brain
13	chr4:190863000-190864400	Flanking Active TSS	Dnd41	blood
14	chr4:190863000-190864800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr4:190863000-190866600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr4:190863000-190880800	Weak transcription	Brain Angular Gyrus	brain
17	chr4:190863200-190864200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr4:190863200-190864200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr4:190863200-190864200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr4:190863200-190864200	Enhancers	Liver	Liver
21	chr4:190863200-190864200	Enhancers	Ovary	ovary
22	chr4:190863200-190864400	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr4:190863200-190864600	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr4:190863200-190864600	Enhancers	Colon Smooth Muscle	Colon
25	chr4:190863200-190864800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr4:190863200-190865000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr4:190863200-190866000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr4:190863200-190866400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr4:190863200-190866400	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr4:190863200-190866400	Weak transcription	Brain Anterior Caudate	brain
31	chr4:190863200-190866400	Weak transcription	Fetal Heart	heart
32	chr4:190863200-190866600	Weak transcription	Stomach Mucosa	stomach
33	chr4:190863200-190866600	Weak transcription	Hela-S3	cervix
34	chr4:190863200-190868800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr4:190863200-190868800	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr4:190863200-190869800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr4:190863200-190869800	Weak transcription	Left Ventricle	heart
38	chr4:190863200-190873800	Weak transcription	Placenta	Placenta
39	chr4:190863200-190874600	Weak transcription	Fetal Intestine Large	intestine
40	chr4:190863200-190875600	Weak transcription	Fetal Thymus	thymus
41	chr4:190863200-190876000	Weak transcription	Stomach Smooth Muscle	stomach
42	chr4:190863200-190876400	Weak transcription	Osteobl	bone
43	chr4:190863200-190879400	Weak transcription	Gastric	stomach
44	chr4:190863200-190880400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr4:190863200-190880400	Weak transcription	Fetal Intestine Small	intestine
46	chr4:190863200-190880800	Weak transcription	HSMMtube	muscle
47	chr4:190863200-190882000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr4:190863400-190864200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr4:190863400-190864200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr4:190863400-190864800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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