Variant report

Variant	rs55936521
Chromosome Location	chr16:70427625-70427626
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:70427347..70429652-chr16:70469861..70473258,4	K562	blood:
2	chr16:70426189..70427824-chr16:70487935..70489664,2	MCF-7	breast:
3	chr16:70425922..70428415-chr16:70432855..70435474,3	K562	blood:
4	chr16:70425305..70429574-chr16:70469861..70473545,6	K562	blood:
5	chr16:70426372..70429310-chr16:70432406..70434780,2	K562	blood:

Variant related genes	Relation type
ENSG00000157353	Chromatin interaction
ENSG00000157350	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	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12149396	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34270587	0.81[AMR][1000 genomes]
rs35567919	0.86[AMR][1000 genomes]
rs35676543	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35878591	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4985409	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985525	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4985526	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56036503	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62049032	0.80[ASN][1000 genomes]
rs72790692	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8063690	0.91[AMR][1000 genomes];0.82[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
rs55936521	RP11-419C5.2	cis	Muscle Skeletal	GTEx
rs55936521	RP11-296I10.6	cis	Muscle Skeletal	GTEx
rs55936521	PDXDC2P	cis	Skin Sun Exposed Lower leg	GTEx
rs55936521	EXOSC6	Cis_1M	lymphoblastoid	RTeQTL
rs55936521	CLEC18C	cis	lung	GTEx
rs55936521	RP11-419C5.2	cis	lung	GTEx
rs55936521	PDXDC2P	cis	Adipose Subcutaneous	GTEx
rs55936521	EXOSC6	cis	Artery Tibial	GTEx
rs55936521	LOC440348	Cis_chr	lymphoblastoid	RTeQTL
rs55936521	RP11-296I10.6	cis	Thyroid	GTEx
rs55936521	CLEC18A	cis	Artery Aorta	GTEx
rs55936521	CLEC18A	cis	Thyroid	GTEx
rs55936521	RP11-419C5.2	cis	Skin Sun Exposed Lower leg	GTEx
rs55936521	RP11-296I10.6	cis	Adipose Subcutaneous	GTEx
rs55936521	CLEC18A	cis	Artery Tibial	GTEx
rs55936521	PDXDC2P	cis	Muscle Skeletal	GTEx
rs55936521	RP11-296I10.6	cis	lung	GTEx
rs55936521	RP11-296I10.6	cis	Artery Tibial	GTEx
rs55936521	CLEC18A	cis	Stomach	GTEx
rs55936521	EXOSC6	cis	Muscle Skeletal	GTEx
rs55936521	RP11-419C5.2	cis	Adipose Subcutaneous	GTEx
rs55936521	CLEC18A	cis	Adipose Subcutaneous	GTEx
rs55936521	RP11-296I10.6	cis	Nerve Tibial	GTEx
rs55936521	RP11-419C5.2	cis	Thyroid	GTEx
rs55936521	PDXDC2P	cis	lung	GTEx
rs55936521	PDXDC2P	cis	Nerve Tibial	GTEx
rs55936521	CLEC18A	cis	Whole Blood	GTEx
rs55936521	CLEC18A	cis	lung	GTEx
rs55936521	CLEC18A	cis	Skin Sun Exposed Lower leg	GTEx
rs55936521	CLEC18C	cis	Whole Blood	GTEx
rs55936521	RP11-419C5.2	cis	Nerve Tibial	GTEx
rs55936521	CLEC18A	cis	Muscle Skeletal	GTEx
rs55936521	RP11-296I10.6	cis	Skin Sun Exposed Lower leg	GTEx
rs55936521	EXOSC6	cis	Whole Blood	GTEx
rs55936521	CLEC18C	cis	Artery Tibial	GTEx
rs55936521	PDXDC2P	cis	Thyroid	GTEx
rs55936521	CLEC18A	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:70415800-70442000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr16:70416000-70429200	Weak transcription	Colonic Mucosa	Colon
3	chr16:70416000-70429400	Weak transcription	Pancreas	Pancrea
4	chr16:70416000-70430000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr16:70416000-70432200	Weak transcription	Gastric	stomach
6	chr16:70416000-70433400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr16:70416000-70435000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr16:70416000-70435600	Strong transcription	Fetal Stomach	stomach
9	chr16:70416000-70437600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr16:70416000-70438000	Weak transcription	Small Intestine	intestine
11	chr16:70416000-70438000	Weak transcription	HUVEC	blood vessel
12	chr16:70416200-70428600	Strong transcription	Fetal Intestine Small	intestine
13	chr16:70416200-70429200	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr16:70416200-70429200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr16:70416200-70432200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr16:70416200-70437000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr16:70416200-70437000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr16:70416400-70434600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr16:70416600-70428800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr16:70416600-70431800	Weak transcription	Brain Angular Gyrus	brain
21	chr16:70420400-70429400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr16:70422000-70429400	Strong transcription	K562	blood
23	chr16:70422400-70430400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr16:70422400-70431800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr16:70422400-70432200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr16:70422600-70430400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr16:70422600-70430400	Weak transcription	Ovary	ovary
28	chr16:70422600-70431800	Weak transcription	Aorta	Aorta
29	chr16:70422600-70432000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr16:70422600-70432000	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr16:70422600-70432000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr16:70422600-70432000	Weak transcription	Brain Substantia Nigra	brain
33	chr16:70422800-70427800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr16:70422800-70429200	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr16:70422800-70430200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr16:70422800-70441400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr16:70422800-70441600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr16:70423000-70428400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr16:70423800-70429000	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr16:70423800-70429800	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr16:70424000-70429200	Strong transcription	Fetal Lung	lung
42	chr16:70424200-70434600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr16:70424400-70429000	Strong transcription	Primary T cells from cord blood	blood
44	chr16:70424400-70429000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr16:70424400-70429400	Strong transcription	GM12878-XiMat	blood
46	chr16:70424400-70430400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr16:70424400-70435400	Strong transcription	HepG2	liver
48	chr16:70424800-70434600	Strong transcription	Fetal Thymus	thymus
49	chr16:70425200-70429200	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr16:70425200-70432000	Weak transcription	Brain Anterior Caudate	brain

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