Variant report

Variant	rs6509552
Chromosome Location	chr19:52075622-52075623
allele	A/G
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	chr19:52075451-52075967	K562	blood:	n/a	n/a
2	SPI1	chr19:52075615-52076071	HL-60	blood:	n/a	n/a
3	FOS	chr19:52075387-52077326	HUVEC	blood vessel:	n/a	n/a
4	MAZ	chr19:52075547-52075850	GM12878	blood:	n/a	n/a
5	MXI1	chr19:52075561-52075843	GM12878	blood:	n/a	n/a
6	POLR2A	chr19:52075563-52076108	K562	blood:	n/a	n/a
7	POLR2A	chr19:52074025-52077434	U87	brain:	n/a	n/a
8	POLR2A	chr19:52075274-52077228	HUVEC	blood vessel:	n/a	n/a
9	EP300	chr19:52075284-52076053	K562	blood:	n/a	chr19:52075824-52075833
10	POLR2A	chr19:52075502-52075992	K562	blood:	n/a	n/a
11	SPI1	chr19:52075601-52076042	GM12891	blood:	n/a	n/a
12	YY1	chr19:52075444-52075970	K562	blood:	n/a	n/a
13	HEY1	chr19:52075544-52075966	K562	blood:	n/a	n/a
14	POLR2A	chr19:52075219-52076089	K562	blood:	n/a	n/a
15	MAZ	chr19:52075176-52076047	K562	blood:	n/a	n/a
16	ATF1	chr19:52075510-52076018	K562	blood:	n/a	n/a
17	STAT5A	chr19:52075593-52076095	K562	blood:	n/a	chr19:52076048-52076059
18	RCOR1	chr19:52074190-52076188	K562	blood:	n/a	n/a
19	ELF1	chr19:52075595-52075996	K562	blood:	n/a	chr19:52075822-52075833 chr19:52075821-52075834
20	POLR2A	chr19:52074059-52077284	PBDE	blood:	n/a	n/a
21	BHLHE40	chr19:52075562-52076309	K562	blood:	n/a	n/a
22	SPI1	chr19:52075558-52076183	HL-60	blood:	n/a	n/a
23	POLR2A	chr19:52075394-52076044	K562	blood:	n/a	n/a
24	JUND	chr19:52075299-52076123	K562	blood:	n/a	n/a
25	SPI1	chr19:52075311-52075989	GM12878	blood:	n/a	n/a
26	ARID3A	chr19:52075575-52076111	K562	blood:	n/a	n/a
27	POLR2A	chr19:52075576-52075980	K562	blood:	n/a	n/a
28	SIN3AK20	chr19:52074917-52075845	K562	blood:	n/a	n/a
29	GATA1	chr19:52074810-52077148	PBDE	blood:	n/a	chr19:52075825-52075835 chr19:52074842-52074853 chr19:52076736-52076745 chr19:52076927-52076934 chr19:52076831-52076840
30	UBTF	chr19:52075458-52076013	K562	blood:	n/a	n/a
31	POLR2A	chr19:52074872-52077276	U87	brain:	n/a	n/a
32	CHD2	chr19:52075594-52075747	K562	blood:	n/a	n/a
33	TBL1XR1	chr19:52075607-52076111	K562	blood:	n/a	n/a
34	MAFK	chr19:52075592-52076127	K562	blood:	n/a	chr19:52075643-52075657
35	PML	chr19:52075569-52076069	K562	blood:	n/a	n/a
36	POLR2A	chr19:52074937-52076991	HUVEC	blood vessel:	n/a	n/a
37	MAX	chr19:52075620-52076116	K562	blood:	n/a	n/a
38	MYC	chr19:52075565-52076136	K562	blood:	n/a	n/a
39	SPI1	chr19:52075599-52075979	GM12878	blood:	n/a	n/a
40	TEAD4	chr19:52074869-52076257	K562	blood:	n/a	n/a
41	POLR2A	chr19:52075327-52076974	HUVEC	blood vessel:	n/a	n/a
42	IRF1	chr19:52075342-52076123	K562	blood:	n/a	n/a
43	ZMIZ1	chr19:52075578-52076043	K562	blood:	n/a	n/a
44	IRF1	chr19:52075356-52076395	K562	blood:	n/a	n/a
45	CTCF	chr19:52075612-52076016	K562	blood:	n/a	chr19:52075786-52075799
46	POLR2A	chr19:52074069-52077434	U87	brain:	n/a	n/a
47	POLR2A	chr19:52074872-52077594	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:51843178..51845619-chr19:52074404..52075904,2	K562	blood:
2	chr19:52073774..52076492-chr19:52083212..52084974,2	K562	blood:
3	chr19:52073066..52077206-chr19:52096074..52099799,4	K562	blood:

Variant related genes	Relation type
ZNF175	TF binding region
ENSG00000167765	Chromatin interaction
ENSG00000186806	Chromatin interaction
ENSG00000105497	Chromatin interaction
ENSG00000267905	Chromatin interaction
ENSG00000269388	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1125620	0.94[JPT][hapmap]
rs1379284	1.00[CEU][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1585160	1.00[CEU][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16982846	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17453522	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2305371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2864106	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2864108	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2864109	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3752129	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap]
rs3752132	1.00[CEU][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4308054	0.84[JPT][hapmap]
rs7245838	1.00[CEU][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7249641	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7257832	0.81[CHD][hapmap]
rs8102214	0.89[JPT][hapmap]
rs8108872	1.00[CEU][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8111685	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066308	chr19:51680133-52103974	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv544049	chr19:51680133-52103974	Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	nsv544051	chr19:51944903-52147459	Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	esv2758504	chr19:51991896-52266700	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	542 gene(s)	inside rSNPs	diseases
5	esv2758767	chr19:51991896-52604625	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	578 gene(s)	inside rSNPs	diseases
6	nsv469584	chr19:52001381-52151821	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv482654	chr19:52001381-52151821	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers 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 miRNA target site	25 gene(s)	inside rSNPs	diseases
8	nsv579966	chr19:52075622-52131119	Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs6509552	ZNF175	Cis_1M	lymphoblastoid	RTeQTL
rs6509552	FCAR	cis	parietal	SCAN
rs6509552	ZNF544	cis	parietal	SCAN
rs6509552	ZNF808	cis	parietal	SCAN
rs6509552	TNNI3	cis	cerebellum	SCAN
rs6509552	ZNF71	cis	cerebellum	SCAN
rs6509552	ZNF175	cis	Esophagus Muscularis	GTEx
rs6509552	ZNF175	cis	multi-tissue	Pritchard
rs6509552	ZNF175	cis	lymphoblastoid	seeQTL
rs6509552	SBK2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52073800-52075800	Active TSS	A549	lung
2	chr19:52074000-52075800	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr19:52074000-52075800	Active TSS	K562	blood
4	chr19:52074000-52076000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr19:52074200-52075800	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr19:52074600-52075800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr19:52074800-52075800	Flanking Active TSS	Adipose Nuclei	Adipose
8	chr19:52074800-52075800	Flanking Active TSS	Liver	Liver
9	chr19:52074800-52075800	Flanking Active TSS	Rectal Smooth Muscle	rectum
10	chr19:52074800-52076000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr19:52074800-52076000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr19:52074800-52076000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr19:52074800-52077400	Flanking Active TSS	HUVEC	blood vessel
14	chr19:52075000-52075800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
15	chr19:52075000-52075800	Flanking Active TSS	Brain Anterior Caudate	brain
16	chr19:52075000-52075800	Flanking Active TSS	Brain Cingulate Gyrus	brain
17	chr19:52075000-52075800	Flanking Active TSS	Brain Hippocampus Middle	brain
18	chr19:52075000-52075800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
19	chr19:52075000-52075800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr19:52075000-52075800	Flanking Active TSS	Fetal Brain Male	brain
21	chr19:52075000-52075800	Flanking Active TSS	Fetal Brain Female	brain
22	chr19:52075000-52075800	Flanking Active TSS	Left Ventricle	heart
23	chr19:52075000-52075800	Flanking Active TSS	Psoas Muscle	Psoas
24	chr19:52075000-52075800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
25	chr19:52075000-52075800	Flanking Active TSS	Dnd41	blood
26	chr19:52075000-52075800	Flanking Active TSS	NHEK	skin
27	chr19:52075000-52076000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr19:52075000-52076000	Flanking Active TSS	Duodenum Mucosa	Duodenum
29	chr19:52075000-52076000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr19:52075000-52076000	Flanking Active TSS	Right Ventricle	heart
31	chr19:52075000-52076000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
32	chr19:52075000-52076000	Flanking Active TSS	HMEC	breast
33	chr19:52075000-52076200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr19:52075000-52076200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr19:52075000-52076200	Flanking Active TSS	NHLF	lung
36	chr19:52075000-52076400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
37	chr19:52075000-52076800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr19:52075000-52077000	Flanking Active TSS	Osteobl	bone
39	chr19:52075200-52075800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr19:52075200-52075800	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr19:52075200-52075800	Enhancers	Primary T cells fromperipheralblood	blood
42	chr19:52075200-52075800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr19:52075200-52075800	Enhancers	Pancreas	Pancrea
44	chr19:52075200-52075800	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr19:52075200-52076000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr19:52075200-52076000	Flanking Active TSS	Brain Germinal Matrix	brain
47	chr19:52075200-52076000	Flanking Active TSS	HSMM	muscle
48	chr19:52075200-52076200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
49	chr19:52075200-52076200	Flanking Active TSS	NH-A	brain
50	chr19:52075200-52076400	Enhancers	Primary B cells from peripheral blood	blood

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