Variant report

Variant	rs6499273
Chromosome Location	chr16:69949787-69949788
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:69944756..69946601-chr16:69948566..69951085,2	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10048088	0.82[ASN][1000 genomes]
rs10048090	0.82[ASN][1000 genomes]
rs11645233	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11647767	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11864678	0.82[ASN][1000 genomes]
rs1566452	0.82[ASN][1000 genomes]
rs2102066	0.82[ASN][1000 genomes]
rs2270840	0.82[ASN][1000 genomes]
rs2270841	0.82[ASN][1000 genomes]
rs2291961	0.82[ASN][1000 genomes]
rs2362643	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3762178	0.82[ASN][1000 genomes]
rs4985376	0.81[EUR][1000 genomes]
rs4985377	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4985378	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4985379	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4985381	0.82[ASN][1000 genomes]
rs4985451	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4985452	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4985453	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4985454	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4985455	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4985456	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4985459	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61611907	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6499272	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7192245	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7192483	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7193518	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7196525	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7206222	0.82[ASN][1000 genomes]
rs8047818	0.82[ASN][1000 genomes]
rs8048590	0.82[ASN][1000 genomes]
rs8048678	0.82[ASN][1000 genomes]
rs8049004	0.82[ASN][1000 genomes]
rs8052727	0.82[ASN][1000 genomes]
rs904804	0.82[ASN][1000 genomes]
rs904805	0.82[ASN][1000 genomes]
rs904806	0.82[ASN][1000 genomes]
rs904807	0.82[ASN][1000 genomes]
rs904809	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs904810	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9922964	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv906823	chr16:69711533-69959223	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6499273	CLEC18A	cis	Whole Blood	GTEx
rs6499273	PDXDC2P	cis	Artery Tibial	GTEx
rs6499273	CLEC18A	cis	Thyroid	GTEx
rs6499273	CLEC18A	cis	lung	GTEx
rs6499273	CLEC18A	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69904200-69951200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr16:69911400-69970200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr16:69913600-69950400	Weak transcription	A549	lung
4	chr16:69923800-69951800	Weak transcription	GM12878-XiMat	blood
5	chr16:69924400-69965000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr16:69925400-69951200	Weak transcription	Fetal Kidney	kidney
7	chr16:69927400-69950200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr16:69935200-69955000	Weak transcription	Colon Smooth Muscle	Colon
9	chr16:69935400-69951000	Weak transcription	Hela-S3	cervix
10	chr16:69938800-69951400	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr16:69939000-69974000	Weak transcription	Fetal Brain Male	brain
12	chr16:69939400-69951200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr16:69939400-69951200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr16:69939600-69967600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr16:69939800-69951200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr16:69940400-69958800	Weak transcription	Right Atrium	heart
17	chr16:69940800-69955000	Weak transcription	Psoas Muscle	Psoas
18	chr16:69941400-69951000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr16:69941400-69951200	Weak transcription	Osteobl	bone
20	chr16:69941600-69950400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr16:69941600-69951000	Weak transcription	HSMMtube	muscle
22	chr16:69941600-69951200	Weak transcription	HSMM	muscle
23	chr16:69941800-69950600	Weak transcription	NHLF	lung
24	chr16:69941800-69951000	Weak transcription	HUVEC	blood vessel
25	chr16:69943200-69951200	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr16:69943200-69951200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr16:69943200-69965600	Weak transcription	Brain Germinal Matrix	brain
28	chr16:69943400-69950000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr16:69943400-69951000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr16:69943400-69951200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr16:69943400-69951200	Weak transcription	HMEC	breast
32	chr16:69943400-69958600	Weak transcription	Rectal Smooth Muscle	rectum
33	chr16:69943400-69959400	Weak transcription	Pancreas	Pancrea
34	chr16:69943600-69950200	Weak transcription	Ovary	ovary
35	chr16:69943600-69950600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr16:69943600-69950600	Weak transcription	Fetal Lung	lung
37	chr16:69943600-69951000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr16:69943600-69951000	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr16:69943600-69951200	Weak transcription	NHEK	skin
40	chr16:69943600-69951600	Weak transcription	Fetal Brain Female	brain
41	chr16:69943600-69951600	Weak transcription	Stomach Smooth Muscle	stomach
42	chr16:69943600-69954800	Weak transcription	Brain Cingulate Gyrus	brain
43	chr16:69943600-69954800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr16:69943600-69955000	Weak transcription	Brain Angular Gyrus	brain
45	chr16:69943600-69958800	Weak transcription	Right Ventricle	heart
46	chr16:69943600-69965000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr16:69943600-69967000	Weak transcription	Small Intestine	intestine
48	chr16:69943800-69951200	Weak transcription	Left Ventricle	heart
49	chr16:69944000-69951000	Weak transcription	NH-A	brain
50	chr16:69944000-69957400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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