Variant report

Variant	rs4985525
Chromosome Location	chr16:70383238-70383239
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:70383140-70383629	GM12878	blood:	n/a	n/a
2	POLR2A	chr16:70383176-70383674	K562	blood:	n/a	n/a
3	HEY1	chr16:70383104-70383497	K562	blood:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:70383005..70385826-chr16:70388585..70390141,2	MCF-7	breast:
2	chr16:70379447..70384942-chr16:70556059..70561583,7	K562	blood:
3	chr16:70365097..70367956-chr16:70382920..70385112,3	K562	blood:
4	chr16:70383049..70384723-chr16:70430171..70432372,2	K562	blood:
5	chr16:70379526..70383319-chr16:70470652..70474068,4	K562	blood:
6	chr16:70375788..70377818-chr16:70381402..70383532,2	K562	blood:
7	chr16:70380932..70385143-chr16:70404657..70409914,6	MCF-7	breast:
8	chr16:70381202..70383601-chr16:70463470..70465382,2	K562	blood:
9	chr16:70382796..70385300-chr16:70408811..70411389,2	K562	blood:
10	chr16:70381919..70383634-chr16:70512388..70514213,2	K562	blood:
11	chr16:70380684..70382606-chr16:70382776..70384424,3	MCF-7	breast:
12	chr16:70382995..70385484-chr16:70556876..70560677,3	MCF-7	breast:
13	chr16:70378223..70384231-chr16:70413255..70416872,7	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000261777	TF binding region
ENSG00000168872	Chromatin interaction
ENSG00000103051	Chromatin interaction
ENSG00000189091	Chromatin interaction
ENSG00000157350	Chromatin interaction
ENSG00000260111	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 47 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1055255	0.84[ASW][hapmap];0.80[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap]
rs1134074	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12149396	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12447090	1.00[ASW][hapmap]
rs17573579	0.83[MKK][hapmap]
rs2070203	0.82[CHD][hapmap]
rs2303791	0.94[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs34087264	0.92[CEU][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap]
rs34270587	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs35567919	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35676543	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35878591	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3811354	0.84[ASW][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap]
rs4985407	0.82[CHD][hapmap]
rs4985409	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4985526	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55936521	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56036503	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7189474	0.82[CHD][hapmap]
rs7192268	0.82[CHD][hapmap]
rs72790692	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8058224	0.82[CHD][hapmap]
rs8062183	0.86[ASW][hapmap]
rs8063690	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482577	chr16:70329048-70516069	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
2	esv3390669	chr16:70363244-70400179	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv833272	chr16:70369769-70569723	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:47)

SNP	Gene	Cis/trans	Tissue	Source
rs4985525	PDXDC2P	cis	Muscle Skeletal	GTEx
rs4985525	EXOSC6	cis	multi-tissue	Pritchard
rs4985525	EXOSC6	cis	parietal	SCAN
rs4985525	CLEC18A	cis	lung	GTEx
rs4985525	RP11-296I10.6	cis	Thyroid	GTEx
rs4985525	CLEC18A	cis	Artery Aorta	GTEx
rs4985525	CLEC18A	cis	Muscle Skeletal	GTEx
rs4985525	RP11-419C5.2	cis	Muscle Skeletal	GTEx
rs4985525	PDXDC2P	cis	parietal	SCAN
rs4985525	RP11-419C5.2	cis	lung	GTEx
rs4985525	CLEC18A	cis	Thyroid	GTEx
rs4985525	WWP2	cis	parietal	SCAN
rs4985525	COG4	cis	lymphoblastoid	seeQTL
rs4985525	PDXDC2P	cis	Nerve Tibial	GTEx
rs4985525	RP11-419C5.2	cis	Skin Sun Exposed Lower leg	GTEx
rs4985525	CLEC18A	cis	Stomach	GTEx
rs4985525	CLEC18A	cis	Adipose Subcutaneous	GTEx
rs4985525	RP11-296I10.6	cis	Skin Sun Exposed Lower leg	GTEx
rs4985525	RP11-296I10.6	cis	Artery Tibial	GTEx
rs4985525	CLEC18C	cis	Artery Tibial	GTEx
rs4985525	CLEC18C	cis	Whole Blood	GTEx
rs4985525	RP11-419C5.2	cis	Nerve Tibial	GTEx
rs4985525	LOC440348	cis	multi-tissue	Pritchard
rs4985525	RP11-296I10.6	cis	Muscle Skeletal	GTEx
rs4985525	PDXDC2P	cis	cerebellum	SCAN
rs4985525	RP11-296I10.6	cis	Adipose Subcutaneous	GTEx
rs4985525	CLEC18A	cis	Skin Sun Exposed Lower leg	GTEx
rs4985525	NFAT5	cis	cerebellum	SCAN
rs4985525	MGC34761	cis	multi-tissue	Pritchard
rs4985525	CLEC18C	cis	lung	GTEx
rs4985525	CLEC18A	cis	Esophagus Mucosa	GTEx
rs4985525	EXOSC6	cis	cerebellum	SCAN
rs4985525	RP11-296I10.6	cis	Nerve Tibial	GTEx
rs4985525	PDXDC2P	cis	Skin Sun Exposed Lower leg	GTEx
rs4985525	RP11-419C5.2	cis	Thyroid	GTEx
rs4985525	PDXDC2P	cis	Thyroid	GTEx
rs4985525	EXOSC6	cis	Artery Tibial	GTEx
rs4985525	PDXDC2P	cis	Adipose Subcutaneous	GTEx
rs4985525	CLEC18A	cis	Artery Tibial	GTEx
rs4985525	LOC440348	Cis_chr	lymphoblastoid	RTeQTL
rs4985525	EXOSC6	Cis_1M	lymphoblastoid	RTeQTL
rs4985525	EXOSC6	cis	Whole Blood	GTEx
rs4985525	RP11-296I10.6	cis	lung	GTEx
rs4985525	EXOSC6	cis	Muscle Skeletal	GTEx
rs4985525	CLEC18A	cis	Whole Blood	GTEx
rs4985525	RP11-419C5.2	cis	Adipose Subcutaneous	GTEx
rs4985525	PDXDC2P	cis	lung	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:70381200-70386200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr16:70381200-70388800	Weak transcription	Spleen	Spleen
3	chr16:70381200-70389200	Weak transcription	Gastric	stomach
4	chr16:70381400-70386600	Weak transcription	Esophagus	oesophagus
5	chr16:70381400-70389000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr16:70381400-70394400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr16:70381600-70383600	Enhancers	Fetal Heart	heart
8	chr16:70381600-70383800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr16:70381600-70384000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr16:70381600-70384400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr16:70381600-70388600	Weak transcription	Aorta	Aorta
12	chr16:70381600-70388600	Weak transcription	Brain Substantia Nigra	brain
13	chr16:70381600-70389000	Weak transcription	Ovary	ovary
14	chr16:70381600-70389200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr16:70381600-70392600	Weak transcription	Fetal Kidney	kidney
16	chr16:70381600-70413200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr16:70381600-70414000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr16:70381800-70383400	Enhancers	Pancreas	Pancrea
19	chr16:70381800-70383600	Genic enhancers	Fetal Muscle Trunk	muscle
20	chr16:70381800-70383600	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr16:70381800-70389000	Weak transcription	HSMMtube	muscle
22	chr16:70382000-70383400	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr16:70382000-70384200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr16:70382000-70387800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr16:70382000-70388600	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr16:70382000-70388800	Weak transcription	Colonic Mucosa	Colon
27	chr16:70382200-70383400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr16:70382200-70383400	Weak transcription	Primary B cells from peripheral blood	blood
29	chr16:70382200-70383400	Enhancers	Muscle Satellite Cultured Cells	--
30	chr16:70382200-70383400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr16:70382200-70383400	Weak transcription	Fetal Brain Female	brain
32	chr16:70382200-70383400	Enhancers	HepG2	liver
33	chr16:70382200-70383400	Enhancers	Osteobl	bone
34	chr16:70382200-70383600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr16:70382200-70383600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr16:70382200-70383600	Enhancers	Pancreatic Islets	Pancreatic Islet
37	chr16:70382200-70384200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr16:70382200-70385000	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr16:70382200-70385200	Weak transcription	Stomach Smooth Muscle	stomach
40	chr16:70382200-70385800	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr16:70382200-70385800	Weak transcription	Rectal Smooth Muscle	rectum
42	chr16:70382200-70386600	Weak transcription	NHLF	lung
43	chr16:70382200-70388400	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr16:70382200-70388600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr16:70382200-70388600	Weak transcription	NH-A	brain
46	chr16:70382200-70389000	Weak transcription	Fetal Brain Male	brain
47	chr16:70382200-70389000	Weak transcription	GM12878-XiMat	blood
48	chr16:70382200-70389000	Weak transcription	HUVEC	blood vessel
49	chr16:70382200-70389200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr16:70382200-70389200	Weak transcription	Rectal Mucosa Donor 31	rectum

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