Variant report

Variant	rs10048129
Chromosome Location	chr16:69966150-69966151
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:69965953-69966180	HepG2	liver:	n/a	n/a
2	POLR2A	chr16:69966092-69966201	H1-hESC	embryonic stem cell:	n/a	n/a

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

Variant related genes	Relation type
WWP2	TF binding region
MIR140	TF binding region
ENSG00000198373	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10048088	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10048090	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1052429	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11864678	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12932078	0.81[EUR][1000 genomes]
rs12932286	0.82[EUR][1000 genomes]
rs1566452	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1983016	0.82[EUR][1000 genomes]
rs2102066	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2270840	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2270841	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2270842	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2291961	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3748388	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3762177	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3762178	0.84[AMR][1000 genomes]
rs4985381	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4985461	0.83[EUR][1000 genomes]
rs7184994	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7206222	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8047818	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8048590	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8048678	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8049004	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8052727	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs904803	0.82[EUR][1000 genomes]
rs904804	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs904805	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs904806	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs904807	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
10	nsv1853	chr16:69962296-70268856	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs10048129	EXOSC6	cis	Muscle Skeletal	GTEx
rs10048129	CLEC18A	cis	Skin Sun Exposed Lower leg	GTEx
rs10048129	PDXDC2P	cis	Artery Tibial	GTEx
rs10048129	PDXDC2P	cis	Nerve Tibial	GTEx
rs10048129	CLEC18C	cis	Nerve Tibial	GTEx
rs10048129	CLEC18A	cis	Esophagus Muscularis	GTEx
rs10048129	CLEC18A	cis	Whole Blood	GTEx
rs10048129	CLEC18A	cis	Thyroid	GTEx
rs10048129	PDXDC2P	cis	Esophagus Muscularis	GTEx
rs10048129	RP11-419C5.2	cis	Nerve Tibial	GTEx
rs10048129	CLEC18A	cis	Adipose Subcutaneous	GTEx
rs10048129	CLEC18A	cis	lung	GTEx
rs10048129	RP11-419C5.2	cis	Artery Tibial	GTEx
rs10048129	CLEC18A	cis	Esophagus Mucosa	GTEx
rs10048129	PDXDC2P	cis	Artery Aorta	GTEx

Chromatin state (count:123 , 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	chr16:69939000-69974000	Weak transcription	Fetal Brain Male	brain
3	chr16:69939600-69967600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr16:69943600-69967000	Weak transcription	Small Intestine	intestine
5	chr16:69945600-69969400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr16:69947600-69977200	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr16:69948200-69977400	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr16:69948400-69977400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr16:69952600-69976000	Weak transcription	Hela-S3	cervix
10	chr16:69952800-69966800	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr16:69953600-69974800	Weak transcription	A549	lung
12	chr16:69954400-69976000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr16:69956400-69975600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr16:69957400-69977400	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr16:69957600-69975400	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr16:69957800-69977200	Strong transcription	Fetal Intestine Small	intestine
17	chr16:69958200-69972800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr16:69958400-69969800	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr16:69958800-69967200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr16:69959000-69976400	Strong transcription	Thymus	Thymus
21	chr16:69959000-69977200	Strong transcription	Fetal Intestine Large	intestine
22	chr16:69959000-69977600	Strong transcription	Primary T cells from cord blood	blood
23	chr16:69959200-69975400	Strong transcription	Duodenum Mucosa	Duodenum
24	chr16:69959400-69976200	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr16:69959600-69975200	Strong transcription	Fetal Thymus	thymus
26	chr16:69959600-69975600	Strong transcription	Fetal Stomach	stomach
27	chr16:69959800-69970400	Weak transcription	HUVEC	blood vessel
28	chr16:69960000-69966400	Weak transcription	Fetal Lung	lung
29	chr16:69960200-69967400	Weak transcription	HMEC	breast
30	chr16:69960200-69969800	Weak transcription	GM12878-XiMat	blood
31	chr16:69960200-69971600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr16:69961400-69967400	Weak transcription	Fetal Kidney	kidney
33	chr16:69961400-69976600	Weak transcription	Right Atrium	heart
34	chr16:69961400-69977000	Weak transcription	HSMM	muscle
35	chr16:69961600-69974800	Weak transcription	Psoas Muscle	Psoas
36	chr16:69961600-69976800	Strong transcription	Spleen	Spleen
37	chr16:69962200-69967600	Weak transcription	NH-A	brain
38	chr16:69962200-69975200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr16:69962400-69976800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr16:69962400-69976800	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr16:69962600-69976800	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr16:69962800-69973200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr16:69962800-69974600	Strong transcription	HepG2	liver
44	chr16:69962800-69975200	Strong transcription	Lung	lung
45	chr16:69962800-69975400	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr16:69962800-69975800	Strong transcription	Colonic Mucosa	Colon
47	chr16:69962800-69975800	Strong transcription	Pancreas	Pancrea
48	chr16:69962800-69976200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr16:69962800-69976200	Strong transcription	Gastric	stomach
50	chr16:69963200-69967400	Genic enhancers	Brain Inferior Temporal Lobe	brain

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