Variant report

Variant	rs8105571
Chromosome Location	chr19:44510341-44510342
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	CEBPB	chr19:44510153-44510520	IMR90	lung:	n/a	chr19:44510299-44510310 chr19:44510327-44510338
2	POLR2A	chr19:44510075-44510534	HL-60	blood:	n/a	n/a
3	STAT3	chr19:44510217-44510361	MCF10A-Er-Src	breast:	n/a	n/a
4	CEBPB	chr19:44510150-44510503	Hela-S3	cervix:	n/a	chr19:44510299-44510310 chr19:44510327-44510338
5	CEBPB	chr19:44510166-44510507	A549	lung:	n/a	chr19:44510299-44510310 chr19:44510327-44510338
6	FOS	chr19:44510302-44510346	MCF10A-Er-Src	breast:	n/a	n/a
7	CEBPB	chr19:44510144-44510506	HepG2	liver:	n/a	chr19:44510299-44510310 chr19:44510327-44510338
8	CEBPB	chr19:44510166-44510468	K562	blood:	n/a	chr19:44510299-44510310 chr19:44510327-44510338
9	SPI1	chr19:44510218-44510523	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:44506934..44508722-chr19:44508906..44511281,4	K562	blood:
2	chr19:44506929..44508722-chr19:44508906..44512991,6	K562	blood:
3	chr19:44507222..44510776-chr19:44517439..44520079,4	MCF-7	breast:

Variant related genes	Relation type
ZNF230	TF binding region
ENSG00000266921	TF binding region
ENSG00000159882	Chromatin interaction
ENSG00000266921	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10418363	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11083732	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11083733	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11881151	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12232810	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1996408	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2191566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2270196	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2356549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35292176	0.88[EUR][1000 genomes]
rs367209	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs367499	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs369106	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs377503	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3810406	0.92[ASW][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs384544	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs390369	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4433920	0.80[ASN][1000 genomes]
rs4482396	0.82[ASN][1000 genomes]
rs4803667	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4803669	0.87[ASN][1000 genomes]
rs4803675	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs55703004	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56101767	0.89[EUR][1000 genomes]
rs56171514	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56317065	0.85[ASN][1000 genomes]
rs59963278	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62115482	0.83[ASN][1000 genomes]
rs62115484	0.81[ASN][1000 genomes]
rs62119173	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62119176	0.90[ASN][1000 genomes]
rs6509133	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6509138	1.00[ASW][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs7245749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7252394	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7253205	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7254261	0.92[ASW][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap]
rs7254907	0.82[ASN][1000 genomes]
rs7255145	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7255315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs7255512	0.95[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs7256908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7258517	1.00[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.87[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7260075	0.80[ASN][1000 genomes]
rs73037629	0.83[ASN][1000 genomes]
rs8104605	0.85[CHB][hapmap];0.85[JPT][hapmap]

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	nsv469650	chr19:44405994-44555426	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs8105571	OPA3	cis	parietal	SCAN
rs8105571	HIF3A	cis	parietal	SCAN
rs8105571	PTGIR	cis	cerebellum	SCAN
rs8105571	OPA3	cis	cerebellum	SCAN
rs8105571	FOXA3	cis	cerebellum	SCAN
rs8105571	CCDC114	cis	cerebellum	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44508000-44510800	Weak transcription	Fetal Muscle Trunk	muscle
2	chr19:44508000-44511000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr19:44508000-44511600	Weak transcription	Pancreas	Pancrea
4	chr19:44508200-44510800	Weak transcription	Brain Hippocampus Middle	brain
5	chr19:44508200-44510800	Weak transcription	Brain Substantia Nigra	brain
6	chr19:44508200-44510800	Weak transcription	Colon Smooth Muscle	Colon
7	chr19:44508200-44511000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr19:44508200-44511000	Weak transcription	Aorta	Aorta
9	chr19:44508200-44511000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr19:44508200-44511000	Weak transcription	Esophagus	oesophagus
11	chr19:44508200-44511000	Weak transcription	Gastric	stomach
12	chr19:44508200-44511000	Weak transcription	Left Ventricle	heart
13	chr19:44508200-44511000	Weak transcription	Ovary	ovary
14	chr19:44508200-44511200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr19:44508200-44511200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr19:44508200-44511400	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr19:44508200-44511400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr19:44508200-44511600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr19:44508200-44511600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr19:44508200-44511600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr19:44508200-44511800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr19:44508200-44511800	Weak transcription	Stomach Mucosa	stomach
23	chr19:44508200-44512000	Weak transcription	HSMM	muscle
24	chr19:44508200-44512800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr19:44508400-44510400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr19:44508400-44510400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr19:44508400-44510400	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr19:44508400-44510600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr19:44508400-44510600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr19:44508400-44510600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr19:44508400-44510600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr19:44508400-44510600	Weak transcription	Duodenum Mucosa	Duodenum
33	chr19:44508400-44510600	Weak transcription	A549	lung
34	chr19:44508400-44510800	Weak transcription	Primary hematopoietic stem cells	blood
35	chr19:44508400-44510800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr19:44508400-44510800	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr19:44508400-44510800	Weak transcription	Rectal Smooth Muscle	rectum
38	chr19:44508400-44510800	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr19:44508400-44510800	Weak transcription	Osteobl	bone
40	chr19:44508400-44511000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr19:44508400-44511000	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr19:44508400-44511000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr19:44508400-44511000	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr19:44508400-44511000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr19:44508400-44511000	Weak transcription	Brain Angular Gyrus	brain
46	chr19:44508400-44511000	Weak transcription	Brain Germinal Matrix	brain
47	chr19:44508400-44511000	Weak transcription	Fetal Brain Female	brain
48	chr19:44508400-44511000	Weak transcription	Fetal Kidney	kidney
49	chr19:44508400-44511000	Weak transcription	Placenta	Placenta
50	chr19:44508400-44511000	Weak transcription	Small Intestine	intestine

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