Variant report

Variant	rs4890617
Chromosome Location	chr18:43622800-43622801
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:29)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:29 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr18:43622417-43623159	SK-N-SH_RA	brain:	n/a	n/a
2	TEAD4	chr18:43622330-43622933	ECC-1	luminal epithelium:	n/a	n/a
3	TEAD4	chr18:43622354-43622955	ECC-1	luminal epithelium:	n/a	n/a
4	RAD21	chr18:43622546-43623117	SK-N-SH_RA	brain:	n/a	n/a
5	NFIC	chr18:43622251-43623021	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr18:43622779-43623186	HL-60	blood:	n/a	n/a
7	PBX3	chr18:43622361-43623266	SK-N-SH	brain:	n/a	n/a
8	NFIC	chr18:43622264-43623092	ECC-1	luminal epithelium:	n/a	n/a
9	NFIC	chr18:43622345-43623196	SK-N-SH	brain:	n/a	n/a
10	TEAD4	chr18:43622419-43623026	SK-N-SH	brain:	n/a	n/a
11	CHD1	chr18:43622704-43622833	GM12878	blood:	n/a	n/a
12	TEAD4	chr18:43622327-43623102	SK-N-SH	brain:	n/a	n/a
13	RUNX3	chr18:43622778-43623152	GM12878	blood:	n/a	n/a
14	TCF12	chr18:43622217-43623377	SK-N-SH	brain:	n/a	n/a
15	FOSL2	chr18:43622324-43623056	SK-N-SH	brain:	n/a	n/a
16	EP300	chr18:43622211-43623295	SK-N-SH	brain:	n/a	n/a
17	EP300	chr18:43622366-43623198	SK-N-SH_RA	brain:	n/a	n/a
18	EP300	chr18:43622253-43623037	ECC-1	luminal epithelium:	n/a	n/a
19	RXRA	chr18:43622441-43623194	SK-N-SH	brain:	n/a	chr18:43622994-43623016
20	RUNX3	chr18:43622713-43623208	GM12878	blood:	n/a	n/a
21	FOS	chr18:43622779-43622930	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr18:43622390-43623031	SK-N-SH	brain:	n/a	n/a
23	TCF12	chr18:43622266-43623329	SK-N-SH	brain:	n/a	n/a
24	NFIC	chr18:43622238-43623197	SK-N-SH	brain:	n/a	n/a
25	GATA3	chr18:43622240-43623341	SK-N-SH	brain:	n/a	n/a
26	JUND	chr18:43622319-43623171	SK-N-SH	brain:	n/a	n/a
27	PBX3	chr18:43622375-43623137	SK-N-SH	brain:	n/a	n/a
28	YY1	chr18:43622434-43622889	ECC-1	luminal epithelium:	n/a	n/a
29	TCF12	chr18:43622311-43623194	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:43621134..43623311-chr18:43651870..43653953,2	K562	blood:
2	chr18:43620677..43623447-chr18:43630437..43631951,2	K562	blood:

No data

Variant related genes	Relation type
PSTPIP2	TF binding region
ENSG00000152229	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11876373	0.85[EUR][1000 genomes]
rs12607480	0.82[CHB][hapmap]
rs12963169	0.88[CEU][hapmap]
rs1866322	0.88[CEU][hapmap]
rs2578184	0.82[EUR][1000 genomes]
rs2578187	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2578189	0.82[CHB][hapmap]
rs2578190	0.80[EUR][1000 genomes]
rs2578193	0.82[EUR][1000 genomes]
rs28372325	0.85[EUR][1000 genomes]
rs2852362	0.82[EUR][1000 genomes]
rs2852363	0.82[EUR][1000 genomes]
rs28524126	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2853801	0.82[EUR][1000 genomes]
rs2853802	0.80[EUR][1000 genomes]
rs28689081	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28805990	0.80[EUR][1000 genomes]
rs35122885	0.82[EUR][1000 genomes]
rs35657986	0.85[EUR][1000 genomes]
rs3744992	0.82[CHB][hapmap];0.80[MEX][hapmap]
rs3753069	0.88[CHD][hapmap];0.81[JPT][hapmap]
rs4243278	0.82[CHB][hapmap]
rs4550555	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs474878	0.82[EUR][1000 genomes]
rs4890312	0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs4890313	1.00[CEU][hapmap];0.86[CHB][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4890314	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4890616	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4890618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4890619	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4890620	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4890624	0.80[EUR][1000 genomes]
rs58397883	0.85[ASN][1000 genomes]
rs60986007	0.85[EUR][1000 genomes]
rs6507663	0.88[ASN][1000 genomes]
rs7226742	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7227301	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8083916	0.81[CHB][hapmap]
rs8085233	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs8096256	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9946543	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9946831	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs9950234	0.91[CHD][hapmap]
rs9950343	1.00[CEU][hapmap];0.86[CHB][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9952157	0.85[EUR][1000 genomes]
rs9954534	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9955008	0.91[CHD][hapmap]
rs9956803	1.00[CEU][hapmap];0.86[CHB][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9957804	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9958257	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9961163	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9964180	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9965365	0.88[CEU][hapmap];0.82[CHB][hapmap]
rs9965812	0.91[CHD][hapmap]
rs9966603	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[ASN][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	nsv1064882	chr18:43558343-43687674	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv543693	chr18:43558343-43687674	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1062024	chr18:43589516-43749410	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv543694	chr18:43589516-43749410	Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:43608600-43651000	Weak transcription	Esophagus	oesophagus
2	chr18:43608800-43631800	Weak transcription	NHLF	lung
3	chr18:43608800-43632000	Weak transcription	Aorta	Aorta
4	chr18:43609000-43631800	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr18:43609000-43631800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr18:43609800-43628000	Weak transcription	Fetal Intestine Small	intestine
7	chr18:43617400-43631800	Weak transcription	Left Ventricle	heart
8	chr18:43618800-43631000	Weak transcription	Liver	Liver
9	chr18:43618800-43631400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr18:43619200-43623400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr18:43619400-43623800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr18:43619600-43622800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr18:43619600-43623800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr18:43619800-43623600	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr18:43619800-43623800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr18:43619800-43623800	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr18:43619800-43623800	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr18:43620000-43623200	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr18:43620000-43623400	Enhancers	Primary T cells fromperipheralblood	blood
20	chr18:43620000-43623600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr18:43620000-43623800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr18:43620000-43623800	Enhancers	HMEC	breast
23	chr18:43620200-43623600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr18:43620200-43623600	Enhancers	Dnd41	blood
25	chr18:43620200-43623800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr18:43620200-43636000	Weak transcription	Lung	lung
27	chr18:43620400-43623400	Enhancers	Primary hematopoietic stem cells	blood
28	chr18:43620400-43623400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr18:43620400-43623400	Enhancers	Fetal Thymus	thymus
30	chr18:43620400-43623600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr18:43620400-43623600	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr18:43620400-43623800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr18:43620600-43623400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr18:43620600-43623600	Enhancers	NHEK	skin
35	chr18:43620600-43624200	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr18:43620800-43623400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr18:43620800-43623600	Enhancers	K562	blood
38	chr18:43621000-43623000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr18:43621200-43623600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr18:43621400-43623600	Enhancers	Primary T cells from cord blood	blood
41	chr18:43621600-43623400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr18:43621600-43623400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
43	chr18:43621800-43622800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
44	chr18:43621800-43622800	Enhancers	HSMMtube	muscle
45	chr18:43621800-43623000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr18:43621800-43623200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr18:43621800-43623400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr18:43621800-43623600	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr18:43621800-43623800	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr18:43622000-43623000	Enhancers	ES-I3 Cell Line	embryonic stem cell

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