Variant report

Variant	rs17246792
Chromosome Location	chr19:38184262-38184263
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr19:38184229-38184513	K562	blood:	n/a	n/a
2	CEBPD	chr19:38184193-38184638	K562	blood:	n/a	n/a
3	TAL1	chr19:38184175-38184549	K562	blood:	n/a	n/a
4	CEBPD	chr19:38184258-38184531	K562	blood:	n/a	n/a
5	EP300	chr19:38184243-38184505	K562	blood:	n/a	n/a
6	PML	chr19:38184155-38184540	K562	blood:	n/a	n/a
7	TEAD4	chr19:38184152-38184524	K562	blood:	n/a	n/a
8	GATA2	chr19:38184167-38184583	K562	blood:	n/a	n/a
9	RCOR1	chr19:38184243-38184502	K562	blood:	n/a	n/a
10	TEAD4	chr19:38184052-38184581	K562	blood:	n/a	n/a

No data

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38145174..38146985-chr19:38184008..38186251,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF781-1	chr19:38184181-38184465	NONHSAT066154

No data

Variant related genes	Relation type
ZNF781	TF binding region
ZFP30	TF binding region
ENSG00000120784	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1060522	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10853710	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11083429	0.80[EUR][1000 genomes]
rs11083433	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11666172	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11668796	0.98[EUR][1000 genomes]
rs11671953	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11673497	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1291	0.96[YRI][hapmap]
rs16975299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28431170	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2891657	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34991303	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55871826	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55913702	0.98[EUR][1000 genomes]
rs55950325	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62108305	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62108351	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6508739	0.98[EUR][1000 genomes]
rs7249622	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7253081	0.81[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7258385	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7259272	0.81[YRI][hapmap]
rs73037060	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8102818	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs17246792	PSG11	cis	cerebellum	SCAN
rs17246792	POU2F2	cis	parietal	SCAN
rs17246792	PHLDB3	cis	parietal	SCAN
rs17246792	IGFL3	cis	cerebellum	SCAN
rs17246792	ZNF573	cis	multi-tissue	Pritchard
rs17246792	AC012309.5	cis	Thyroid	GTEx
rs17246792	PHLDB3	cis	cerebellum	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38182200-38184400	Active TSS	Brain Hippocampus Middle	brain
2	chr19:38182400-38184400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr19:38183200-38208800	Weak transcription	Fetal Heart	heart
4	chr19:38183400-38187400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr19:38183400-38187400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr19:38183400-38187400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr19:38183400-38188800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr19:38183400-38190000	Weak transcription	Stomach Mucosa	stomach
9	chr19:38183600-38184400	Enhancers	Primary hematopoietic stem cells	blood
10	chr19:38183600-38184400	Enhancers	Brain Cingulate Gyrus	brain
11	chr19:38183600-38184800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr19:38183600-38186400	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr19:38183600-38187200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr19:38183600-38187200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr19:38183600-38187400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr19:38183600-38187400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr19:38183600-38187400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr19:38183600-38187400	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr19:38183600-38187400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr19:38183600-38187400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr19:38183600-38187400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr19:38183600-38187400	Weak transcription	Aorta	Aorta
23	chr19:38183600-38187400	Weak transcription	Brain Germinal Matrix	brain
24	chr19:38183600-38187400	Weak transcription	Fetal Intestine Large	intestine
25	chr19:38183600-38187400	Weak transcription	Fetal Intestine Small	intestine
26	chr19:38183600-38187400	Weak transcription	Fetal Muscle Leg	muscle
27	chr19:38183600-38187400	Weak transcription	Left Ventricle	heart
28	chr19:38183600-38187400	Weak transcription	Ovary	ovary
29	chr19:38183600-38187400	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr19:38183600-38187400	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr19:38183600-38187400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr19:38183600-38187400	Weak transcription	Right Ventricle	heart
33	chr19:38183600-38187400	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr19:38183600-38187400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr19:38183600-38187400	Weak transcription	Spleen	Spleen
36	chr19:38183600-38187400	Weak transcription	NHLF	lung
37	chr19:38183600-38187600	Weak transcription	Primary T cells from cord blood	blood
38	chr19:38183600-38187600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr19:38183600-38187600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr19:38183600-38187800	Weak transcription	Primary B cells from cord blood	blood
41	chr19:38183600-38187800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr19:38183600-38188000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr19:38183600-38188800	Weak transcription	Fetal Kidney	kidney
44	chr19:38183600-38189400	Weak transcription	Psoas Muscle	Psoas
45	chr19:38183600-38190000	Weak transcription	Small Intestine	intestine
46	chr19:38183800-38184400	Enhancers	HepG2	liver
47	chr19:38183800-38187400	Weak transcription	Fetal Brain Female	brain
48	chr19:38183800-38187400	Weak transcription	Fetal Muscle Trunk	muscle
49	chr19:38183800-38187600	Weak transcription	Placenta	Placenta
50	chr19:38183800-38187600	Weak transcription	Fetal Thymus	thymus

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