Variant report

Variant	rs4239528
Chromosome Location	chr19:44562928-44562929
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	CTCF	chr19:44562920-44563070	HAc	cerebellar:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:44561763..44564477-chr19:44574561..44577058,2	MCF-7	breast:

Variant related genes	Relation type
ZNF223	TF binding region
ENSG00000186026	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11083734	0.83[ASN][1000 genomes]
rs11083735	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11083736	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11083737	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666432	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12610472	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1474061	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1996409	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2138823	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2138824	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2176431	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35120085	0.83[ASN][1000 genomes]
rs382197	0.86[EUR][1000 genomes]
rs3826941	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs427608	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4299256	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4371266	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4375771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4444434	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs451388	0.92[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes]
rs454904	0.92[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4550576	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4555257	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4580302	0.82[ASN][1000 genomes]
rs4803668	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4803672	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4803674	0.85[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55798868	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56003307	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56230322	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56250154	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57895932	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62115491	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62119177	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6509135	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6509137	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6509139	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7251015	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7252213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7255192	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7257809	0.92[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8105003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8109313	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8109615	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8110348	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9646633	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833840	chr19:44520620-44715760	Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs4239528	EMP3	cis	parietal	SCAN
rs4239528	ZNF223	cis	Adipose Subcutaneous	GTEx
rs4239528	APOE	cis	parietal	SCAN
rs4239528	CLPTM1	cis	cerebellum	SCAN
rs4239528	FUT2	cis	parietal	SCAN
rs4239528	ETFB	cis	parietal	SCAN
rs4239528	C19orf73	cis	cerebellum	SCAN
rs4239528	ZNF223	cis	Skin Sun Exposed Lower leg	GTEx
rs4239528	OPA3	cis	parietal	SCAN
rs4239528	ZNF613	cis	parietal	SCAN
rs4239528	ZNF223	cis	Thyroid	GTEx
rs4239528	ASPDH	cis	cerebellum	SCAN
rs4239528	ZNF223	cis	lung	GTEx
rs4239528	SNORD34	cis	parietal	SCAN
rs4239528	HIF3A	cis	parietal	SCAN
rs4239528	ZNF223	cis	Nerve Tibial	GTEx
rs4239528	KPTN	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44556600-44564600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr19:44557000-44565000	Weak transcription	Psoas Muscle	Psoas
3	chr19:44557000-44566800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:44557000-44567400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr19:44557000-44567400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr19:44557000-44567600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr19:44557000-44568800	Weak transcription	HMEC	breast
8	chr19:44557000-44570200	Weak transcription	HUVEC	blood vessel
9	chr19:44557000-44570200	Weak transcription	NHDF-Ad	bronchial
10	chr19:44557000-44575600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr19:44557200-44565600	Weak transcription	NHLF	lung
12	chr19:44557400-44564400	Weak transcription	Fetal Heart	heart
13	chr19:44557400-44565000	Weak transcription	Small Intestine	intestine
14	chr19:44557400-44565000	Weak transcription	NH-A	brain
15	chr19:44557400-44570000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr19:44557400-44570200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr19:44557600-44564800	Weak transcription	Fetal Brain Male	brain
18	chr19:44558200-44571800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr19:44558200-44573200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr19:44558200-44575600	ZNF genes & repeats	Liver	Liver
21	chr19:44558800-44563800	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr19:44558800-44567800	Strong transcription	Stomach Smooth Muscle	stomach
23	chr19:44558800-44572800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
24	chr19:44559000-44565200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
25	chr19:44559200-44563000	Strong transcription	Ovary	ovary
26	chr19:44559200-44569000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr19:44559200-44569000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr19:44559200-44569400	Strong transcription	Fetal Stomach	stomach
29	chr19:44559400-44565400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr19:44559400-44565800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr19:44559400-44569400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr19:44559400-44570000	Weak transcription	Stomach Mucosa	stomach
33	chr19:44559600-44563600	Strong transcription	Adipose Nuclei	Adipose
34	chr19:44559600-44565800	Strong transcription	Colonic Mucosa	Colon
35	chr19:44559800-44563200	Strong transcription	Colon Smooth Muscle	Colon
36	chr19:44559800-44563600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr19:44559800-44568600	Strong transcription	HSMMtube	muscle
38	chr19:44560000-44563600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
39	chr19:44560000-44568800	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr19:44560200-44567200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr19:44560400-44563200	Weak transcription	Fetal Kidney	kidney
42	chr19:44560400-44564600	Weak transcription	Primary B cells from cord blood	blood
43	chr19:44560400-44564600	Weak transcription	Primary B cells from peripheral blood	blood
44	chr19:44560400-44566400	Weak transcription	Fetal Thymus	thymus
45	chr19:44560400-44566800	Weak transcription	NHEK	skin
46	chr19:44560800-44569400	Strong transcription	Fetal Intestine Large	intestine
47	chr19:44560800-44570000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr19:44561000-44568800	Strong transcription	Fetal Brain Female	brain
49	chr19:44561000-44569200	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr19:44561200-44569600	Strong transcription	HUES6 Cell Line	embryonic stem cell

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