Variant report

Variant	rs6564409
Chromosome Location	chr16:77223750-77223751
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10781982	0.89[AMR][1000 genomes]
rs11149970	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11649440	0.89[AMR][1000 genomes]
rs12447059	0.81[AMR][1000 genomes]
rs12448094	1.00[CHB][hapmap]
rs12716823	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2113282	1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2161715	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs2232504	1.00[CHB][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2232509	1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2241415	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2241416	1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2278045	1.00[CHB][hapmap];0.84[JPT][hapmap];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34143201	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3743759	1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3743761	1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3743762	1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3760004	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3760005	1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3760006	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3760007	1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4887893	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs62049594	0.81[AMR][1000 genomes]
rs6420403	0.91[AMR][1000 genomes]
rs6564404	1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs6564405	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6564406	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6564407	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6564408	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7185297	1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7185889	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7194408	0.81[AMR][1000 genomes]
rs7195255	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7202265	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7204238	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7205119	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8047912	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs8048285	0.89[CHB][hapmap]
rs8052509	0.89[CHB][hapmap]
rs8062063	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs9923489	0.92[AMR][1000 genomes]
rs9924160	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9924694	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9930201	0.89[AMR][1000 genomes]
rs9930541	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9939130	1.00[CHB][hapmap];0.91[AMR][1000 genomes]
rs9939212	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869201	chr16:76714549-77233646	Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv1057677	chr16:76861946-77230013	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1065343	chr16:76927295-77279747	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv542965	chr16:76927295-77279747	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv1055234	chr16:77003426-77467286	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
6	nsv1065048	chr16:77003426-77675163	Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
7	esv2830376	chr16:77014551-77658185	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
8	nsv1065149	chr16:77032082-77671890	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
9	nsv1062349	chr16:77039764-77458731	Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
10	nsv542967	chr16:77039764-77458731	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
11	nsv1056676	chr16:77139682-77854848	Strong transcription Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
12	nsv906954	chr16:77197633-77227180	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
13	nsv827756	chr16:77198788-77225812	Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
14	nsv906955	chr16:77202701-77227180	Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6564409	MON1B	cis	Whole Blood	GTEx
rs6564409	SYCE1L	cis	Artery Tibial	GTEx
rs6564409	SYCE1L	cis	Thyroid	GTEx
rs6564409	SYCE1L	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:77222000-77223800	Enhancers	HepG2	liver
2	chr16:77222600-77224000	Enhancers	Primary T helper naive cells from peripheral blood	blood
3	chr16:77223200-77223800	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr16:77223200-77226200	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr16:77223400-77223800	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr16:77223400-77223800	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr16:77223400-77223800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr16:77223400-77223800	Flanking Active TSS	GM12878-XiMat	blood
9	chr16:77223400-77224000	Enhancers	Primary T cells fromperipheralblood	blood
10	chr16:77223400-77224000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr16:77223400-77224200	Flanking Active TSS	Dnd41	blood
12	chr16:77223400-77226600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr16:77223600-77223800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr16:77223600-77223800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr16:77223600-77223800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr16:77223600-77224000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr16:77223600-77224000	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr16:77223600-77224000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr16:77223600-77224000	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr16:77223600-77224000	Enhancers	Fetal Muscle Trunk	muscle
21	chr16:77223600-77224000	Enhancers	Lung	lung
22	chr16:77223600-77225600	Active TSS	iPS-18 Cell Line	embryonic stem cell
23	chr16:77223600-77226200	Active TSS	H1 Cell Line	embryonic stem cell

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