Variant report

Variant	rs12149320
Chromosome Location	chr16:69959821-69959822
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:69957939..69963004-chr16:69963560..69969238,6	K562	blood:
2	chr16:69957701..69959225-chr16:69959260..69961035,2	K562	blood:

Variant related genes	Relation type
ENSG00000208017	Chromatin interaction
ENSG00000198373	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs2133796	0.85[ASN][1000 genomes]
rs2270843	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3192882	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4985460	0.82[EUR][1000 genomes]
rs57613728	0.85[ASN][1000 genomes]
rs62053265	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062171	chr16:69854267-70188585	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats 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 miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv542941	chr16:69854267-70188585	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1059249	chr16:69854467-70188446	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription 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 miRNA target site	63 gene(s)	inside rSNPs	diseases
4	nsv542942	chr16:69854467-70188446	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
5	esv2758428	chr16:69855122-70313222	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
6	esv2758652	chr16:69855122-70313222	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
7	esv1792580	chr16:69950347-70005207	Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	esv1801278	chr16:69951043-70050770	Enhancers Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
9	esv1829103	chr16:69951043-70050770	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:37)

SNP	Gene	Cis/trans	Tissue	Source
rs12149320	CLEC18A	cis	Esophagus Muscularis	GTEx
rs12149320	PDXDC2P	cis	Muscle Skeletal	GTEx
rs12149320	PDXDC2P	cis	lung	GTEx
rs12149320	CLEC18C	cis	lung	GTEx
rs12149320	CLEC18C	cis	Thyroid	GTEx
rs12149320	CLEC18A	cis	Artery Aorta	GTEx
rs12149320	CLEC18A	cis	Stomach	GTEx
rs12149320	RP11-296I10.6	cis	Muscle Skeletal	GTEx
rs12149320	CLEC18A	cis	Adipose Subcutaneous	GTEx
rs12149320	RP11-419C5.2	cis	Esophagus Muscularis	GTEx
rs12149320	RP11-419C5.2	cis	Adipose Subcutaneous	GTEx
rs12149320	PDXDC2P	cis	Artery Tibial	GTEx
rs12149320	RP11-419C5.2	cis	Artery Tibial	GTEx
rs12149320	RP11-419C5.2	cis	Nerve Tibial	GTEx
rs12149320	EXOSC6	cis	Artery Tibial	GTEx
rs12149320	PDXDC2P	cis	Stomach	GTEx
rs12149320	RP11-419C5.2	cis	Artery Aorta	GTEx
rs12149320	CLEC18A	cis	Muscle Skeletal	GTEx
rs12149320	RP11-419C5.2	cis	Muscle Skeletal	GTEx
rs12149320	PDXDC2P	cis	Esophagus Muscularis	GTEx
rs12149320	RP11-419C5.2	cis	Thyroid	GTEx
rs12149320	RP11-419C5.2	cis	Skin Sun Exposed Lower leg	GTEx
rs12149320	RP11-419C5.2	cis	lung	GTEx
rs12149320	EXOSC6	cis	Muscle Skeletal	GTEx
rs12149320	LOC440348	Cis_chr	lymphoblastoid	RTeQTL
rs12149320	CLEC18C	cis	Whole Blood	GTEx
rs12149320	PDXDC2P	cis	Nerve Tibial	GTEx
rs12149320	PDXDC2P	cis	Thyroid	GTEx
rs12149320	CLEC18A	cis	Whole Blood	GTEx
rs12149320	CLEC18A	cis	Thyroid	GTEx
rs12149320	CLEC18A	cis	Artery Tibial	GTEx
rs12149320	RP11-419C5.2	cis	Stomach	GTEx
rs12149320	PDXDC2P	cis	Skin Sun Exposed Lower leg	GTEx
rs12149320	CLEC18A	cis	lung	GTEx
rs12149320	PDXDC2P	cis	Adipose Subcutaneous	GTEx
rs12149320	CLEC18A	cis	Skin Sun Exposed Lower leg	GTEx
rs12149320	CLEC18A	cis	Esophagus Mucosa	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69911400-69970200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr16:69924400-69965000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr16:69939000-69974000	Weak transcription	Fetal Brain Male	brain
4	chr16:69939600-69967600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr16:69943200-69965600	Weak transcription	Brain Germinal Matrix	brain
6	chr16:69943600-69965000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr16:69943600-69967000	Weak transcription	Small Intestine	intestine
8	chr16:69945200-69964600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr16:69945400-69964000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr16:69945600-69969400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr16:69947600-69977200	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr16:69948200-69977400	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr16:69948400-69977400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr16:69952200-69961000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr16:69952200-69965000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr16:69952400-69963800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr16:69952600-69963600	Weak transcription	NHEK	skin
18	chr16:69952600-69976000	Weak transcription	Hela-S3	cervix
19	chr16:69952800-69963200	Weak transcription	Fetal Brain Female	brain
20	chr16:69952800-69965000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr16:69952800-69966800	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr16:69953600-69974800	Weak transcription	A549	lung
23	chr16:69954000-69961200	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr16:69954400-69976000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr16:69955600-69961200	Weak transcription	Psoas Muscle	Psoas
26	chr16:69955800-69960400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr16:69956400-69975600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr16:69957400-69961000	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr16:69957400-69964400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr16:69957400-69977400	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr16:69957600-69975400	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr16:69957800-69960000	Enhancers	Fetal Muscle Trunk	muscle
33	chr16:69957800-69960200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr16:69957800-69962200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr16:69957800-69977200	Strong transcription	Fetal Intestine Small	intestine
36	chr16:69958000-69965000	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr16:69958000-69965000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr16:69958200-69960400	Weak transcription	Brain Substantia Nigra	brain
39	chr16:69958200-69965000	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr16:69958200-69965000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr16:69958200-69965200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr16:69958200-69965600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr16:69958200-69972800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr16:69958400-69963000	Weak transcription	Fetal Heart	heart
45	chr16:69958400-69963800	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr16:69958400-69969800	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr16:69958600-69960200	Flanking Active TSS	Osteobl	bone
48	chr16:69958600-69961200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr16:69958800-69960000	Enhancers	Placenta Amnion	Placenta Amnion
50	chr16:69958800-69960200	Flanking Active TSS	NHLF	lung

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