Variant report

Variant	rs1060506
Chromosome Location	chr16:31133449-31133450
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	chr16:31133433-31133783	HepG2	liver:	n/a	n/a
2	POLR2A	chr16:31133366-31133692	K562	blood:	n/a	n/a
3	POLR2A	chr16:31133445-31133504	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr16:31132186-31133474	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:31127220..31133615-chr16:31189948..31195209,18	K562	blood:
2	chr16:31132115..31134271-chr16:31191509..31194298,2	K562	blood:

Variant related genes	Relation type
KAT8	TF binding region
ENSG00000089280	Chromatin interaction
ENSG00000260304	Chromatin interaction

Extended variants
information (count: 137 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs10782001	0.89[JPT][hapmap]
rs10782002	0.89[JPT][hapmap]
rs10871454	1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11076	0.88[JPT][hapmap]
rs1108431	0.84[ASN][1000 genomes]
rs11150600	0.89[JPT][hapmap]
rs11150601	0.89[JPT][hapmap]
rs11150604	1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11640534	0.89[JPT][hapmap]
rs11640767	0.82[ASN][1000 genomes]
rs11640957	0.82[ASN][1000 genomes]
rs11640961	0.89[JPT][hapmap]
rs11642192	0.93[ASN][1000 genomes]
rs11647284	0.95[ASN][1000 genomes]
rs11647442	1.00[ASN][1000 genomes]
rs11862744	1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[ASN][1000 genomes]
rs11864806	0.95[ASN][1000 genomes]
rs11864839	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11865038	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[ASN][1000 genomes]
rs11865499	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12102776	0.82[CHB][hapmap];0.92[CHD][hapmap]
rs12445650	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12448321	0.84[ASN][1000 genomes]
rs12597511	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12716981	1.00[ASN][1000 genomes]
rs12716982	1.00[ASN][1000 genomes]
rs12928852	0.89[JPT][hapmap]
rs12931046	0.89[JPT][hapmap]
rs12934418	0.84[ASN][1000 genomes]
rs13708	0.89[JPT][hapmap]
rs14235	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1458202	0.89[JPT][hapmap]
rs1549293	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1549299	0.87[EUR][1000 genomes]
rs17839567	0.84[ASN][1000 genomes]
rs17839568	0.95[ASN][1000 genomes]
rs1870293	0.89[JPT][hapmap]
rs1978485	1.00[ASN][1000 genomes]
rs1978487	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2032915	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2054213	0.89[JPT][hapmap]
rs2288004	0.84[ASN][1000 genomes]
rs2303222	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2303223	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2305880	0.89[JPT][hapmap]
rs2305884	0.89[JPT][hapmap]
rs2359612	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2855475	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs28725459	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28814987	0.95[ASN][1000 genomes]
rs2884738	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34649473	0.81[ASN][1000 genomes]
rs35351013	0.89[ASN][1000 genomes]
rs35468353	1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[ASN][1000 genomes]
rs35675346	0.84[GIH][hapmap];1.00[JPT][hapmap]
rs35713203	0.95[ASN][1000 genomes]
rs3751855	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4468641	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[ASN][1000 genomes]
rs4527034	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4889525	0.89[JPT][hapmap]
rs4889530	0.82[ASN][1000 genomes]
rs4889599	0.89[JPT][hapmap]
rs4889603	0.89[JPT][hapmap]
rs4889604	0.89[JPT][hapmap]
rs4889606	0.89[JPT][hapmap]
rs4889609	1.00[JPT][hapmap];0.82[MEX][hapmap]
rs4889619	0.88[ASN][1000 genomes]
rs4889620	1.00[ASN][1000 genomes]
rs4889623	0.82[CHB][hapmap]
rs55667375	0.83[EUR][1000 genomes]
rs55766044	1.00[ASN][1000 genomes]
rs55979739	0.84[ASN][1000 genomes]
rs56284083	0.84[ASN][1000 genomes]
rs56314408	1.00[ASN][1000 genomes]
rs56813533	0.89[ASN][1000 genomes]
rs57434408	0.86[ASN][1000 genomes]
rs58726213	0.82[ASN][1000 genomes]
rs59061704	0.82[ASN][1000 genomes]
rs59735493	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60996860	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61162043	0.95[ASN][1000 genomes]
rs61320757	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6565217	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[ASN][1000 genomes]
rs6950	0.89[JPT][hapmap]
rs7187995	0.89[ASN][1000 genomes]
rs7190802	0.82[CHB][hapmap]
rs7196161	0.95[ASN][1000 genomes]
rs7196726	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7197717	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[ASN][1000 genomes]
rs7199949	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7200879	0.84[GIH][hapmap];1.00[JPT][hapmap]
rs7203999	0.82[CHD][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap]
rs7204459	0.89[JPT][hapmap]
rs7206511	0.89[JPT][hapmap]
rs7294	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs729482	1.00[JPT][hapmap]
rs732172	1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs732173	0.84[ASN][1000 genomes]
rs73530203	0.93[ASN][1000 genomes]
rs749670	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs749671	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs749767	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7500176	0.84[ASN][1000 genomes]
rs750952	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs8047803	0.95[ASN][1000 genomes]
rs8050588	0.89[JPT][hapmap]
rs8050894	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs8056842	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs8060857	0.89[JPT][hapmap]
rs8061047	0.89[ASN][1000 genomes]
rs8062719	0.89[JPT][hapmap]
rs881929	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs889548	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs889555	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs897986	0.89[JPT][hapmap]
rs9923231	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9925964	1.00[ASN][1000 genomes]
rs9926533	0.82[CHD][hapmap];0.89[JPT][hapmap]
rs9929899	0.82[ASN][1000 genomes]
rs9934438	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9936329	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9939417	1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9939558	0.84[ASN][1000 genomes]
rs9972727	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062456	chr16:30442166-31253997	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
2	nsv542898	chr16:30442166-31253997	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
3	nsv905729	chr16:30642867-31247924	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	387 gene(s)	inside rSNPs	diseases
4	nsv431451	chr16:30682399-31340999	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
5	nsv905734	chr16:30877544-31191482	Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
6	nsv905735	chr16:30890538-31247924	Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	264 gene(s)	inside rSNPs	diseases
7	nsv457483	chr16:30903679-31191482	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	253 gene(s)	inside rSNPs	diseases
8	nsv571820	chr16:30903679-31191482	Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	253 gene(s)	inside rSNPs	diseases
9	esv1797877	chr16:30948643-31188432	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
10	nsv833193	chr16:30960796-31133604	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
11	nsv905740	chr16:31066249-31232437	Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	202 gene(s)	inside rSNPs	diseases
12	nsv905741	chr16:31066249-31247924	Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	202 gene(s)	inside rSNPs	diseases
13	nsv905742	chr16:31102321-31247924	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	188 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1060506	MYST1	cis	parietal	SCAN
rs1060506	KAT8	cis	Artery Tibial	GTEx
rs1060506	MYST1	cis	lymphoblastoid	seeQTL
rs1060506	MYST1	Cis_1M	lymphoblastoid	RTeQTL
rs1060506	KAT8	cis	Skin Sun Exposed Lower leg	GTEx
rs1060506	VKORC1	cis	cerebellum	SCAN
rs1060506	YPEL3	cis	parietal	SCAN
rs1060506	MYST1	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31130200-31133800	Strong transcription	HUES48 Cell Line	embryonic stem cell
2	chr16:31130200-31133800	Strong transcription	Brain Germinal Matrix	brain
3	chr16:31130200-31134000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr16:31130200-31135600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr16:31130200-31136600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr16:31130400-31133800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr16:31130400-31133800	Strong transcription	Primary hematopoietic stem cells	blood
8	chr16:31130400-31134200	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr16:31130400-31134400	Strong transcription	Fetal Lung	lung
10	chr16:31130400-31135800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr16:31130400-31137200	Weak transcription	Stomach Mucosa	stomach
12	chr16:31130400-31139000	Strong transcription	Fetal Thymus	thymus
13	chr16:31130400-31139800	Strong transcription	Fetal Muscle Trunk	muscle
14	chr16:31130400-31140400	Strong transcription	Stomach Smooth Muscle	stomach
15	chr16:31130400-31145000	Strong transcription	Fetal Brain Female	brain
16	chr16:31130400-31153000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr16:31130600-31134000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr16:31130600-31134000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr16:31130600-31134000	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr16:31130600-31134000	Strong transcription	K562	blood
21	chr16:31130600-31134200	Strong transcription	Brain Hippocampus Middle	brain
22	chr16:31130600-31134200	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr16:31130600-31135600	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr16:31130600-31135600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr16:31130600-31135600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr16:31130600-31135800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr16:31130600-31135800	Strong transcription	Dnd41	blood
28	chr16:31130600-31136200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr16:31130600-31136400	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr16:31130600-31136600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr16:31130600-31136600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr16:31130600-31136800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr16:31130600-31136800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr16:31130600-31138600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr16:31130600-31138600	Strong transcription	Fetal Intestine Small	intestine
36	chr16:31130600-31138800	Strong transcription	Fetal Intestine Large	intestine
37	chr16:31130600-31139000	Strong transcription	Fetal Muscle Leg	muscle
38	chr16:31130600-31139600	Strong transcription	Adipose Nuclei	Adipose
39	chr16:31130600-31140600	Weak transcription	Right Atrium	heart
40	chr16:31130600-31144400	Strong transcription	Primary B cells from peripheral blood	blood
41	chr16:31130600-31144800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr16:31130600-31144800	Strong transcription	Thymus	Thymus
43	chr16:31130600-31145000	Weak transcription	Fetal Heart	heart
44	chr16:31130600-31145200	Strong transcription	Fetal Stomach	stomach
45	chr16:31130800-31134200	Strong transcription	Brain Inferior Temporal Lobe	brain
46	chr16:31130800-31135800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr16:31130800-31139400	Strong transcription	Primary T cells from cord blood	blood
48	chr16:31130800-31143800	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr16:31130800-31144200	Strong transcription	Liver	Liver
50	chr16:31130800-31145000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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