Variant report

Variant	rs13143
Chromosome Location	chr16:31489033-31489034
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:31486386..31493720-chr16:31496174..31501149,12	MCF-7	breast:
2	chr16:31486411..31490471-chr16:31517300..31521270,7	K562	blood:
3	chr16:31488206..31490925-chr16:31493306..31495304,2	MCF-7	breast:
4	chr16:31489000..31489500-chr19:2303503..2304060,2	NB4	blood:
5	chr16:31198671..31201560-chr16:31487722..31489477,2	K562	blood:
6	chr16:31487738..31490319-chr16:31724484..31726664,2	K562	blood:
7	chr16:31487154..31492170-chr16:31516854..31521226,9	K562	blood:
8	chr16:31487920..31490610-chr16:31726146..31728854,2	K562	blood:
9	chr16:31466606..31474995-chr16:31481116..31490982,25	MCF-7	breast:
10	chr16:31487495..31490933-chr16:31720453..31723394,4	MCF-7	breast:
11	chr16:31486749..31489738-chr16:31518463..31521140,5	MCF-7	breast:
12	chr16:31479635..31481245-chr16:31488025..31490096,2	MCF-7	breast:
13	chr16:31465649..31475592-chr16:31481764..31491028,24	MCF-7	breast:
14	chr16:31486327..31489778-chr16:31498037..31501156,4	K562	blood:
15	chr16:31487832..31489561-chr16:31724526..31726086,2	MCF-7	breast:
16	chr16:31485287..31490245-chr16:31497773..31501253,8	MCF-7	breast:
17	chr16:31487843..31490472-chr16:31518223..31521167,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000140691	Chromatin interaction
ENSG00000260740	Chromatin interaction
ENSG00000197302	Chromatin interaction
ENSG00000260625	Chromatin interaction
ENSG00000140675	Chromatin interaction
ENSG00000140688	Chromatin interaction
ENSG00000260267	Chromatin interaction
ENSG00000261731	Chromatin interaction
ENSG00000089280	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11150626	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.91[LWK][hapmap];0.83[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11865835	0.94[CEU][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13337037	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.83[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34081766	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3934739	1.00[ASW][hapmap];0.94[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.91[LWK][hapmap];0.83[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4519345	0.90[JPT][hapmap]
rs4889548	0.92[JPT][hapmap]
rs4889673	0.92[JPT][hapmap]
rs6565235	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6565236	0.94[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6565242	0.92[JPT][hapmap];0.81[YRI][hapmap]
rs7188278	0.94[CEU][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8057401	0.92[JPT][hapmap]
rs8062314	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9926717	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9934336	1.00[ASW][hapmap];0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.91[LWK][hapmap];0.83[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9935222	0.92[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3392534	chr16:31303038-31573066	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	104 gene(s)	inside rSNPs	diseases
2	nsv833194	chr16:31358179-31528545	Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
3	nsv905747	chr16:31394179-31888684	Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	123 gene(s)	inside rSNPs	diseases
4	nsv905748	chr16:31427678-31559220	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	94 gene(s)	inside rSNPs	diseases
5	nsv905749	chr16:31427678-31565597	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	96 gene(s)	inside rSNPs	diseases
6	nsv905750	chr16:31427678-31587662	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	98 gene(s)	inside rSNPs	diseases
7	nsv905751	chr16:31431360-31489033	Bivalent Enhancer Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	82 gene(s)	inside rSNPs	diseases
8	nsv905752	chr16:31436932-31565597	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	95 gene(s)	inside rSNPs	diseases
9	nsv905753	chr16:31436932-31587662	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
10	nsv905754	chr16:31451699-31565597	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs13143	AHSP	cis	parietal	SCAN
rs13143	SLC5A2	cis	lung	GTEx
rs13143	ENSG00000140682	cis	multi-tissue	Pritchard
rs13143	AC026471.6	cis	lung	GTEx
rs13143	TAOK2	cis	parietal	SCAN
rs13143	FBXL19	cis	cerebellum	SCAN
rs13143	PRR14	cis	cerebellum	SCAN
rs13143	INO80E	cis	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31484400-31489200	Enhancers	Fetal Heart	heart
2	chr16:31484400-31489400	Genic enhancers	Fetal Muscle Trunk	muscle
3	chr16:31484400-31492000	Weak transcription	Right Atrium	heart
4	chr16:31484600-31489400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr16:31484800-31489400	Strong transcription	Ovary	ovary
6	chr16:31484800-31489600	Strong transcription	Aorta	Aorta
7	chr16:31485000-31490000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr16:31485000-31490800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr16:31485200-31489600	Strong transcription	Right Ventricle	heart
10	chr16:31485200-31489800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr16:31485200-31490600	Weak transcription	HSMMtube	muscle
12	chr16:31485600-31489400	Strong transcription	A549	lung
13	chr16:31485600-31489600	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr16:31485800-31489600	Strong transcription	Left Ventricle	heart
15	chr16:31485800-31491200	Strong transcription	Muscle Satellite Cultured Cells	--
16	chr16:31486200-31490000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr16:31486200-31491000	Strong transcription	Osteobl	bone
18	chr16:31486400-31490600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr16:31486400-31491400	Strong transcription	NHLF	lung
20	chr16:31486600-31490400	Strong transcription	Adipose Nuclei	Adipose
21	chr16:31486600-31490800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr16:31486600-31491200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr16:31486600-31491400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr16:31486600-31495800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr16:31486800-31495800	Weak transcription	HMEC	breast
26	chr16:31487200-31489200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
27	chr16:31487200-31489400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
28	chr16:31487400-31489200	Bivalent Enhancer	Fetal Brain Male	brain
29	chr16:31487400-31489400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr16:31487400-31489400	Active TSS	H9 Cell Line	embryonic stem cell
31	chr16:31487400-31489400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr16:31487400-31493400	Weak transcription	HSMM	muscle
33	chr16:31487600-31489200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr16:31487600-31489200	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr16:31487600-31489400	Transcr. at gene 5' and 3'	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr16:31487600-31489400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
37	chr16:31487600-31489400	Active TSS	Primary T killer memory cells from peripheral blood	blood
38	chr16:31487600-31489600	Active TSS	iPS-15b Cell Line	embryonic stem cell
39	chr16:31487600-31491800	Weak transcription	NHDF-Ad	bronchial
40	chr16:31487800-31489200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
41	chr16:31487800-31489200	Flanking Active TSS	Primary hematopoietic stem cells	blood
42	chr16:31487800-31489200	Active TSS	Brain Hippocampus Middle	brain
43	chr16:31487800-31489400	Transcr. at gene 5' and 3'	Fetal Adrenal Gland	Adrenal Gland
44	chr16:31487800-31489400	Transcr. at gene 5' and 3'	Placenta	Placenta
45	chr16:31488000-31489200	Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr16:31488000-31489200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr16:31488000-31489200	Flanking Active TSS	Fetal Thymus	thymus
48	chr16:31488000-31489200	Active TSS	K562	blood
49	chr16:31488200-31489200	Active TSS	H1 Cell Line	embryonic stem cell
50	chr16:31488200-31489200	Active TSS	Colonic Mucosa	Colon

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