Variant report

Variant	rs4985409
Chromosome Location	chr16:70418843-70418844
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:70416879..70419217-chr16:70428815..70431051,2	K562	blood:
2	chr16:70411913..70419512-chr16:70432088..70435360,7	MCF-7	breast:
3	chr16:70408723..70414559-chr16:70414602..70419341,6	K562	blood:

Variant related genes	Relation type
ENSG00000157350	Chromatin interaction
ENSG00000260111	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 37 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1134074	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12149396	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34270587	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs35567919	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs35676543	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35878591	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4985525	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];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55936521	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56036503	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62049032	0.80[ASN][1000 genomes]
rs72790692	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8063690	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	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:37)

SNP	Gene	Cis/trans	Tissue	Source
rs4985409	LOC440348	Cis_chr	lymphoblastoid	RTeQTL
rs4985409	RP11-419C5.2	cis	Nerve Tibial	GTEx
rs4985409	CLEC18A	cis	Adipose Subcutaneous	GTEx
rs4985409	RP11-419C5.2	cis	Adipose Subcutaneous	GTEx
rs4985409	EXOSC6	cis	Whole Blood	GTEx
rs4985409	PDXDC2P	cis	Adipose Subcutaneous	GTEx
rs4985409	RP11-296I10.6	cis	Thyroid	GTEx
rs4985409	PDXDC2P	cis	lung	GTEx
rs4985409	RP11-419C5.2	cis	Thyroid	GTEx
rs4985409	CLEC18C	cis	Whole Blood	GTEx
rs4985409	CLEC18A	cis	Skin Sun Exposed Lower leg	GTEx
rs4985409	RP11-296I10.6	cis	Nerve Tibial	GTEx
rs4985409	CLEC18A	cis	Esophagus Mucosa	GTEx
rs4985409	CLEC18A	cis	Artery Aorta	GTEx
rs4985409	CLEC18A	cis	Whole Blood	GTEx
rs4985409	CLEC18A	cis	Stomach	GTEx
rs4985409	CLEC18C	cis	Artery Tibial	GTEx
rs4985409	PDXDC2P	cis	Nerve Tibial	GTEx
rs4985409	RP11-296I10.6	cis	Adipose Subcutaneous	GTEx
rs4985409	CLEC18C	cis	lung	GTEx
rs4985409	PDXDC2P	cis	Skin Sun Exposed Lower leg	GTEx
rs4985409	CLEC18A	cis	lung	GTEx
rs4985409	RP11-296I10.6	cis	Skin Sun Exposed Lower leg	GTEx
rs4985409	RP11-419C5.2	cis	Muscle Skeletal	GTEx
rs4985409	RP11-296I10.6	cis	Artery Tibial	GTEx
rs4985409	RP11-419C5.2	cis	Skin Sun Exposed Lower leg	GTEx
rs4985409	EXOSC6	Cis_1M	lymphoblastoid	RTeQTL
rs4985409	RP11-296I10.6	cis	Muscle Skeletal	GTEx
rs4985409	RP11-296I10.6	cis	lung	GTEx
rs4985409	PDXDC2P	cis	Muscle Skeletal	GTEx
rs4985409	CLEC18A	cis	Thyroid	GTEx
rs4985409	PDXDC2P	cis	Thyroid	GTEx
rs4985409	CLEC18A	cis	Artery Tibial	GTEx
rs4985409	CLEC18A	cis	Muscle Skeletal	GTEx
rs4985409	EXOSC6	cis	Muscle Skeletal	GTEx
rs4985409	EXOSC6	cis	Artery Tibial	GTEx
rs4985409	RP11-419C5.2	cis	lung	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:70415800-70427600	Weak transcription	Fetal Kidney	kidney
2	chr16:70415800-70442000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr16:70416000-70419200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr16:70416000-70420400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr16:70416000-70420600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr16:70416000-70420600	Weak transcription	Aorta	Aorta
7	chr16:70416000-70421000	Weak transcription	Left Ventricle	heart
8	chr16:70416000-70421200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr16:70416000-70421200	Weak transcription	NH-A	brain
10	chr16:70416000-70421600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr16:70416000-70421600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr16:70416000-70421600	Weak transcription	Ovary	ovary
13	chr16:70416000-70421600	Weak transcription	Psoas Muscle	Psoas
14	chr16:70416000-70421800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr16:70416000-70421800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr16:70416000-70421800	Weak transcription	Lung	lung
17	chr16:70416000-70422000	Weak transcription	NHDF-Ad	bronchial
18	chr16:70416000-70422000	Weak transcription	NHLF	lung
19	chr16:70416000-70422200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr16:70416000-70424400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr16:70416000-70425000	Weak transcription	Right Atrium	heart
22	chr16:70416000-70425800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr16:70416000-70425800	Weak transcription	Colon Smooth Muscle	Colon
24	chr16:70416000-70425800	Weak transcription	Osteobl	bone
25	chr16:70416000-70429200	Weak transcription	Colonic Mucosa	Colon
26	chr16:70416000-70429400	Weak transcription	Pancreas	Pancrea
27	chr16:70416000-70430000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr16:70416000-70432200	Weak transcription	Gastric	stomach
29	chr16:70416000-70433400	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr16:70416000-70435000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr16:70416000-70435600	Strong transcription	Fetal Stomach	stomach
32	chr16:70416000-70437600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr16:70416000-70438000	Weak transcription	Small Intestine	intestine
34	chr16:70416000-70438000	Weak transcription	HUVEC	blood vessel
35	chr16:70416200-70419200	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr16:70416200-70419200	Weak transcription	Liver	Liver
37	chr16:70416200-70419200	Weak transcription	GM12878-XiMat	blood
38	chr16:70416200-70419400	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr16:70416200-70419400	Weak transcription	Primary T cells from cord blood	blood
40	chr16:70416200-70421000	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr16:70416200-70421000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr16:70416200-70421000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr16:70416200-70421000	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr16:70416200-70421000	Weak transcription	Brain Germinal Matrix	brain
45	chr16:70416200-70421000	Weak transcription	Brain Hippocampus Middle	brain
46	chr16:70416200-70421200	Weak transcription	Brain Cingulate Gyrus	brain
47	chr16:70416200-70421200	Weak transcription	Right Ventricle	heart
48	chr16:70416200-70421600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr16:70416200-70421600	Weak transcription	Duodenum Mucosa	Duodenum
50	chr16:70416200-70421800	Weak transcription	Primary B cells from peripheral blood	blood

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