Variant report

Variant	rs384059
Chromosome Location	chr4:87982790-87982791
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:87980531..87986351-chr4:87988282..87991075,4	K562	blood:
2	chr4:87980531..87984297-chr4:87985969..87990791,4	K562	blood:
3	chr4:87977551..87981344-chr4:87982047..87984756,4	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10018897	0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10516789	0.93[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs168204	0.93[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs1841265	0.82[AMR][1000 genomes]
rs19026	0.93[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs236674	0.90[ASN][1000 genomes]
rs236675	0.93[CHB][hapmap];0.93[CHD][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs236678	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs236685	0.90[ASN][1000 genomes]
rs236686	0.93[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs236687	0.90[ASN][1000 genomes]
rs2869642	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2926512	0.92[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs3116679	0.90[ASN][1000 genomes]
rs342436	0.86[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs342457	0.93[CHB][hapmap];0.93[CHD][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs342458	0.87[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs342459	0.87[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs342460	0.93[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs342461	0.87[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs342462	0.87[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs342465	0.93[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs3775225	0.93[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs3822042	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs390604	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs393991	0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs411365	0.81[ASN][1000 genomes]
rs447990	0.86[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs60757751	0.88[ASN][1000 genomes]
rs6827213	1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9992235	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv999176	chr4:87869996-88098136	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv998335	chr4:87869996-88104414	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1001017	chr4:87872160-88087003	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv537166	chr4:87872160-88087003	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv999098	chr4:87899091-88016048	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv537167	chr4:87899091-88016048	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv997750	chr4:87933945-88264127	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv879525	chr4:87964363-88033352	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs384059	PTPN13	cis	cerebellum	SCAN
rs384059	HSD17B11	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87964600-87995000	Weak transcription	Hela-S3	cervix
2	chr4:87968800-87983400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr4:87968800-87995000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr4:87969000-87994600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr4:87970200-87989800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr4:87975000-87987800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr4:87976200-87989800	Weak transcription	Fetal Muscle Trunk	muscle
8	chr4:87977000-87989400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr4:87978200-87983000	Enhancers	Stomach Smooth Muscle	stomach
10	chr4:87978200-87983600	Enhancers	Psoas Muscle	Psoas
11	chr4:87979000-87983400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr4:87979400-87983600	Strong transcription	Dnd41	blood
13	chr4:87979600-87983000	Strong transcription	HepG2	liver
14	chr4:87979600-87990000	Weak transcription	Aorta	Aorta
15	chr4:87979800-87983200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr4:87979800-87984000	Strong transcription	Primary B cells from cord blood	blood
17	chr4:87979800-87989600	Weak transcription	Fetal Muscle Leg	muscle
18	chr4:87979800-87991800	Weak transcription	A549	lung
19	chr4:87980000-87990000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr4:87980000-87994000	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr4:87980200-87983600	Strong transcription	Fetal Thymus	thymus
22	chr4:87980200-87983600	Enhancers	Rectal Smooth Muscle	rectum
23	chr4:87980200-87989800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr4:87980400-87982800	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr4:87980400-87983600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr4:87980400-87988800	Weak transcription	Fetal Kidney	kidney
27	chr4:87980400-87989400	Weak transcription	Fetal Lung	lung
28	chr4:87980400-87989600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr4:87980600-87987400	Weak transcription	Lung	lung
30	chr4:87980600-87988400	Weak transcription	Brain Anterior Caudate	brain
31	chr4:87980600-87989800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr4:87980800-87982800	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr4:87980800-87984800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr4:87980800-87988000	Weak transcription	Fetal Heart	heart
35	chr4:87980800-87991000	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr4:87981000-87983000	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr4:87981000-87983000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr4:87981000-87983800	Strong transcription	Primary hematopoietic stem cells	blood
39	chr4:87981000-87984200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr4:87981000-87988200	Weak transcription	Adipose Nuclei	Adipose
41	chr4:87981000-87988600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr4:87981000-87989800	Weak transcription	Brain Cingulate Gyrus	brain
43	chr4:87981000-87994600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr4:87981200-87983000	Enhancers	Muscle Satellite Cultured Cells	--
45	chr4:87981200-87983600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr4:87981200-87983600	Strong transcription	Placenta	Placenta
47	chr4:87981200-87987600	Weak transcription	Brain Substantia Nigra	brain
48	chr4:87981200-87988400	Weak transcription	Ovary	ovary
49	chr4:87981200-87988600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr4:87981200-87989600	Weak transcription	Brain Angular Gyrus	brain

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