Variant report

Variant	rs28733806
Chromosome Location	chr16:70335323-70335324
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:70331932..70334361-chr16:70334943..70337402,2	MCF-7	breast:
2	chr16:70321820..70325241-chr16:70331601..70337689,10	MCF-7	breast:
3	chr16:70321807..70326700-chr16:70327142..70336316,14	MCF-7	breast:
4	chr16:70326803..70329805-chr16:70331309..70336594,5	K562	blood:
5	chr16:70320811..70326767-chr16:70331299..70339483,12	K562	blood:

Variant related genes	Relation type
ENSG00000090861	Chromatin interaction
ENSG00000260537	Chromatin interaction
ENSG00000157349	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 43 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs2070203	0.90[ASN][1000 genomes]
rs34087264	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34270587	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35567919	0.84[EUR][1000 genomes]
rs4985407	0.83[ASN][1000 genomes]
rs66627085	0.83[AMR][1000 genomes]
rs7192268	0.85[ASN][1000 genomes]
rs775208	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833271	chr16:70185694-70353334	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv906871	chr16:70302333-70375873	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv906872	chr16:70303418-70356746	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv960356	chr16:70318585-70339325	Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:43)

SNP	Gene	Cis/trans	Tissue	Source
rs28733806	RP11-419C5.2	cis	Muscle Skeletal	GTEx
rs28733806	RP11-419C5.2	cis	Skin Sun Exposed Lower leg	GTEx
rs28733806	RP11-296I10.6	cis	lung	GTEx
rs28733806	AARS	Cis_1M	lymphoblastoid	RTeQTL
rs28733806	CLEC18A	cis	Esophagus Mucosa	GTEx
rs28733806	CLEC18A	cis	Artery Tibial	GTEx
rs28733806	RP11-419C5.2	cis	Nerve Tibial	GTEx
rs28733806	CLEC18A	cis	Artery Aorta	GTEx
rs28733806	EXOSC6	cis	Skin Sun Exposed Lower leg	GTEx
rs28733806	RP11-296I10.6	cis	Muscle Skeletal	GTEx
rs28733806	PDXDC2P	cis	Adipose Subcutaneous	GTEx
rs28733806	CLEC18C	cis	Nerve Tibial	GTEx
rs28733806	CLEC18A	cis	Skin Sun Exposed Lower leg	GTEx
rs28733806	RP11-419C5.2	cis	Thyroid	GTEx
rs28733806	EXOSC6	cis	Muscle Skeletal	GTEx
rs28733806	EXOSC6	cis	lung	GTEx
rs28733806	CLEC18A	cis	Whole Blood	GTEx
rs28733806	EXOSC6	cis	Artery Tibial	GTEx
rs28733806	CLEC18C	cis	lung	GTEx
rs28733806	CLEC18A	cis	Thyroid	GTEx
rs28733806	RP11-296I10.6	cis	Skin Sun Exposed Lower leg	GTEx
rs28733806	CLEC18A	cis	Adipose Subcutaneous	GTEx
rs28733806	CLEC18C	cis	Thyroid	GTEx
rs28733806	RP11-419C5.2	cis	lung	GTEx
rs28733806	RP11-296I10.6	cis	Adipose Subcutaneous	GTEx
rs28733806	PDXDC2P	cis	lung	GTEx
rs28733806	RP11-419C5.2	cis	Adipose Subcutaneous	GTEx
rs28733806	EXOSC6	cis	Heart Left Ventricle	GTEx
rs28733806	LOC440348	Cis_chr	lymphoblastoid	RTeQTL
rs28733806	EXOSC6	Cis_1M	lymphoblastoid	RTeQTL
rs28733806	RP11-296I10.6	cis	Artery Tibial	GTEx
rs28733806	CLEC18A	cis	Stomach	GTEx
rs28733806	RP11-296I10.6	cis	Whole Blood	GTEx
rs28733806	CLEC18C	cis	Artery Tibial	GTEx
rs28733806	CLEC18A	cis	lung	GTEx
rs28733806	RP11-296I10.6	cis	Nerve Tibial	GTEx
rs28733806	RP11-296I10.6	cis	Esophagus Muscularis	GTEx
rs28733806	PDXDC2P	cis	Thyroid	GTEx
rs28733806	PDXDC2P	cis	Skin Sun Exposed Lower leg	GTEx
rs28733806	PDXDC2P	cis	Muscle Skeletal	GTEx
rs28733806	CLEC18A	cis	Muscle Skeletal	GTEx
rs28733806	PDXDC2P	cis	Nerve Tibial	GTEx
rs28733806	CLEC18C	cis	Whole Blood	GTEx

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:70333800-70335600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr16:70333800-70336600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr16:70333800-70343800	Weak transcription	Lung	lung
4	chr16:70333800-70348800	Weak transcription	Placenta	Placenta
5	chr16:70333800-70349600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr16:70333800-70350200	Weak transcription	Gastric	stomach
7	chr16:70333800-70350800	Weak transcription	Aorta	Aorta
8	chr16:70333800-70367800	Weak transcription	Small Intestine	intestine
9	chr16:70334000-70335400	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr16:70334000-70335400	Weak transcription	Psoas Muscle	Psoas
11	chr16:70334000-70335600	Weak transcription	Fetal Lung	lung
12	chr16:70334000-70336200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
13	chr16:70334000-70337000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr16:70334000-70338800	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr16:70334000-70339000	Weak transcription	Primary T cells from cord blood	blood
16	chr16:70334000-70348800	Weak transcription	Brain Hippocampus Middle	brain
17	chr16:70334000-70349400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr16:70334000-70349400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr16:70334000-70349400	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr16:70334000-70349400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr16:70334000-70349400	Weak transcription	HSMMtube	muscle
22	chr16:70334000-70349800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr16:70334000-70349800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr16:70334000-70349800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr16:70334000-70349800	Weak transcription	Fetal Muscle Trunk	muscle
26	chr16:70334000-70349800	Weak transcription	Ovary	ovary
27	chr16:70334000-70349800	Weak transcription	Right Ventricle	heart
28	chr16:70334000-70349800	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr16:70334000-70350200	Weak transcription	Left Ventricle	heart
30	chr16:70334000-70350400	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr16:70334000-70368400	Weak transcription	Fetal Heart	heart
32	chr16:70334200-70335400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr16:70334200-70335600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr16:70334200-70337800	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr16:70334200-70338800	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr16:70334200-70338800	Weak transcription	HMEC	breast
37	chr16:70334200-70338800	Weak transcription	NHEK	skin
38	chr16:70334200-70349800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr16:70334200-70349800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr16:70334200-70350000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr16:70334200-70379800	Weak transcription	Stomach Mucosa	stomach
42	chr16:70334400-70335600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
43	chr16:70334400-70335600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
44	chr16:70334400-70335800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr16:70334400-70335800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr16:70334400-70335800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr16:70334400-70335800	ZNF genes & repeats	Brain Germinal Matrix	brain
48	chr16:70334400-70335800	ZNF genes & repeats	Thymus	Thymus
49	chr16:70334400-70335800	ZNF genes & repeats	GM12878-XiMat	blood
50	chr16:70334400-70336000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast

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