Variant report

Variant	rs4985452
Chromosome Location	chr16:69945141-69945142
allele	C/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: 64 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10048088	0.86[ASN][1000 genomes]
rs10048090	0.86[ASN][1000 genomes]
rs1052429	0.83[CHD][hapmap];0.81[ASN][1000 genomes]
rs10852461	0.82[CHB][hapmap]
rs11075746	0.82[ASN][1000 genomes]
rs11645233	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11647767	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11864678	0.86[ASN][1000 genomes]
rs12932078	0.81[ASN][1000 genomes]
rs1566452	0.83[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1983016	0.83[CHD][hapmap]
rs2102066	0.86[ASN][1000 genomes]
rs2270840	0.86[ASN][1000 genomes]
rs2270841	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2270842	0.83[CHD][hapmap]
rs2291961	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2362643	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2362658	1.00[JPT][hapmap]
rs3748388	0.83[CHD][hapmap];0.81[ASN][1000 genomes]
rs3762177	0.83[CHD][hapmap]
rs3762178	0.86[ASN][1000 genomes]
rs4985376	0.91[EUR][1000 genomes]
rs4985377	0.92[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4985378	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4985379	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4985381	0.86[ASN][1000 genomes]
rs4985451	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985453	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985454	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4985455	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4985456	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4985459	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4985461	0.81[ASN][1000 genomes]
rs61611907	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6499272	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6499273	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7184994	0.81[ASN][1000 genomes]
rs7192245	0.85[AMR][1000 genomes]
rs7192483	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7193518	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7196525	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7206222	0.86[ASN][1000 genomes]
rs8047818	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs8048590	0.83[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs8048678	0.83[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs8049004	0.86[ASN][1000 genomes]
rs8052727	0.86[ASN][1000 genomes]
rs904803	1.00[JPT][hapmap]
rs904804	0.86[ASN][1000 genomes]
rs904805	0.86[ASN][1000 genomes]
rs904806	0.86[ASN][1000 genomes]
rs904807	0.83[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs904808	1.00[JPT][hapmap]
rs904809	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs904810	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9302605	0.81[ASN][1000 genomes]
rs9922964	0.83[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:21)

SNP	Gene	Cis/trans	Tissue	Source
rs4985452	CLEC18A	cis	Adipose Subcutaneous	GTEx
rs4985452	PDXDC2P	cis	Artery Tibial	GTEx
rs4985452	CBFB	cis	parietal	SCAN
rs4985452	CLEC18A	cis	Whole Blood	GTEx
rs4985452	LOC440349	cis	multi-tissue	Pritchard
rs4985452	PION	trans	brain	seeQTL
rs4985452	COG4	cis	brain	seeQTL
rs4985452	CLEC18A	cis	Thyroid	GTEx
rs4985452	ZNF669	trans	brain	seeQTL
rs4985452	EXOSC6	cis	multi-tissue	Pritchard
rs4985452	DSN1	trans	brain	seeQTL
rs4985452	PDE4C	trans	brain	seeQTL
rs4985452	LOC497190	cis	multi-tissue	Pritchard
rs4985452	STK4	trans	brain	seeQTL
rs4985452	MGC34761	cis	multi-tissue	Pritchard
rs4985452	KLHL28	trans	brain	seeQTL
rs4985452	CES8	cis	parietal	SCAN
rs4985452	SULT1A1	trans	brain	seeQTL
rs4985452	CLEC18A	cis	lung	GTEx
rs4985452	SLFN5	trans	brain	seeQTL
rs4985452	PDXDC2P	cis	parietal	SCAN

Chromatin state (count:117 , 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	chr16:69923800-69949200	Weak transcription	Dnd41	blood
5	chr16:69923800-69951800	Weak transcription	GM12878-XiMat	blood
6	chr16:69924400-69965000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr16:69925400-69951200	Weak transcription	Fetal Kidney	kidney
8	chr16:69927400-69950200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr16:69934800-69946600	Strong transcription	Primary T cells from cord blood	blood
10	chr16:69934800-69946800	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr16:69934800-69946800	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr16:69935200-69946000	Strong transcription	Primary B cells from cord blood	blood
13	chr16:69935200-69955000	Weak transcription	Colon Smooth Muscle	Colon
14	chr16:69935400-69951000	Weak transcription	Hela-S3	cervix
15	chr16:69938800-69951400	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr16:69939000-69946800	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr16:69939000-69974000	Weak transcription	Fetal Brain Male	brain
18	chr16:69939200-69945800	Strong transcription	Duodenum Mucosa	Duodenum
19	chr16:69939400-69951200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr16:69939400-69951200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr16:69939600-69967600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr16:69939800-69951200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr16:69940400-69946000	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr16:69940400-69958800	Weak transcription	Right Atrium	heart
25	chr16:69940800-69955000	Weak transcription	Psoas Muscle	Psoas
26	chr16:69941000-69945600	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr16:69941000-69945800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr16:69941000-69946400	Strong transcription	Primary B cells from peripheral blood	blood
29	chr16:69941200-69946400	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr16:69941400-69945200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr16:69941400-69951000	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr16:69941400-69951200	Weak transcription	Osteobl	bone
33	chr16:69941600-69946000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr16:69941600-69950400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr16:69941600-69951000	Weak transcription	HSMMtube	muscle
36	chr16:69941600-69951200	Weak transcription	HSMM	muscle
37	chr16:69941800-69946400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr16:69941800-69950600	Weak transcription	NHLF	lung
39	chr16:69941800-69951000	Weak transcription	HUVEC	blood vessel
40	chr16:69942200-69945400	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr16:69942200-69946000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr16:69942200-69946000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr16:69942200-69946400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr16:69942400-69945200	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr16:69942400-69945400	Strong transcription	Fetal Intestine Large	intestine
46	chr16:69942400-69945600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr16:69942400-69945600	Strong transcription	Thymus	Thymus
48	chr16:69942400-69946000	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr16:69942400-69946000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr16:69942400-69946200	Strong transcription	Sigmoid Colon	Sigmoid Colon

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