Variant report

Variant	rs919778
Chromosome Location	chr19:19772722-19772723
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:108)
CpG islands
(count:61)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:108 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	YY1	chr19:19772451-19773027	GM12892	blood:	n/a	n/a
2	EBF1	chr19:19772552-19773184	GM12878	blood:	n/a	chr19:19773079-19773088 chr19:19772924-19772935 chr19:19773078-19773088
3	POLR2A	chr19:19772031-19775125	GM19193	blood:	n/a	n/a
4	POLR2A	chr19:19772640-19775184	Raji	blood:	n/a	n/a
5	POLR2A	chr19:19772616-19772926	HepG2	liver:	n/a	n/a
6	POLR2A	chr19:19771886-19774863	GM12878	blood:	n/a	n/a
7	SPI1	chr19:19772646-19773173	HL-60	blood:	n/a	chr19:19772932-19772939 chr19:19772929-19772942
8	RCOR1	chr19:19772150-19772994	GM12878	blood:	n/a	n/a
9	POLR2A	chr19:19772026-19775170	GM18505	blood:	n/a	n/a
10	CREB1	chr19:19772345-19773083	GM12878	blood:	n/a	chr19:19772685-19772698
11	POLR2A	chr19:19772545-19775164	GM18526	blood:	n/a	n/a
12	POLR2A	chr19:19772089-19775169	GM18951	blood:	n/a	n/a
13	POLR2A	chr19:19772425-19775227	PFSK-1	brain:	n/a	n/a
14	POLR2A	chr19:19772506-19775176	GM12878	blood:	n/a	n/a
15	PML	chr19:19772639-19773057	GM12878	blood:	n/a	n/a
16	POLR2A	chr19:19771866-19775239	GM12892	blood:	n/a	n/a
17	EP300	chr19:19772440-19773036	GM12878	blood:	n/a	n/a
18	POU2F2	chr19:19772366-19773608	GM12878	blood:	n/a	n/a
19	SPI1	chr19:19772645-19773072	GM12891	blood:	n/a	chr19:19772932-19772939 chr19:19772929-19772942
20	POLR2A	chr19:19772336-19773649	GM12878	blood:	n/a	n/a
21	CEBPB	chr19:19772529-19773327	GM12878	blood:	n/a	n/a
22	NFATC1	chr19:19772242-19773224	GM12878	blood:	n/a	n/a
23	SIN3A	chr19:19772433-19773066	GM12878	blood:	n/a	n/a
24	MXI1	chr19:19771963-19775426	SK-N-SH	brain:	n/a	chr19:19774765-19774780 chr19:19774550-19774565
25	EBF1	chr19:19772505-19772985	GM12878	blood:	n/a	chr19:19772924-19772935
26	WRNIP1	chr19:19772134-19774816	GM12878	blood:	n/a	n/a
27	TAF1	chr19:19772612-19773117	GM12891	blood:	n/a	n/a
28	POLR2A	chr19:19771901-19775139	K562	blood:	n/a	n/a
29	POLR2A	chr19:19772159-19775226	GM12878	blood:	n/a	n/a
30	RELA	chr19:19772604-19773173	GM15510	blood:	n/a	n/a
31	POLR2A	chr19:19772681-19774998	HepG2	liver:	n/a	n/a
32	EBF1	chr19:19772587-19773239	GM12878	blood:	n/a	chr19:19773079-19773088 chr19:19772924-19772935 chr19:19773078-19773088
33	STAT3	chr19:19772648-19773772	GM12878	blood:	n/a	n/a
34	BHLHE40	chr19:19772514-19773180	GM12878	blood:	n/a	n/a
35	POLR2A	chr19:19771894-19774978	GM12891	blood:	n/a	n/a
36	POLR2A	chr19:19772531-19774868	GM12891	blood:	n/a	n/a
37	CHD2	chr19:19772513-19773410	GM12878	blood:	n/a	n/a
38	STAT5A	chr19:19772285-19774087	GM12878	blood:	n/a	n/a
39	IRF1	chr19:19772673-19773224	K562	blood:	n/a	n/a
40	TAF1	chr19:19772601-19773129	GM12878	blood:	n/a	n/a
41	POLR2A	chr19:19771960-19774921	GM12892	blood:	n/a	n/a
42	FOXM1	chr19:19772414-19773021	GM12878	blood:	n/a	n/a
43	YY1	chr19:19772579-19772977	SK-N-SH_RA	brain:	n/a	n/a
44	SP1	chr19:19772565-19773083	GM12878	blood:	n/a	n/a
45	CTCF	chr19:19772494-19772763	GM12878	blood:	n/a	n/a
46	MTA3	chr19:19772639-19773331	GM12878	blood:	n/a	n/a
47	PML	chr19:19772238-19773454	GM12878	blood:	n/a	n/a
48	FOXM1	chr19:19772414-19773153	GM12878	blood:	n/a	n/a
49	SPI1	chr19:19772606-19773104	GM12891	blood:	n/a	chr19:19772932-19772939 chr19:19772929-19772942
50	YY1	chr19:19772621-19773014	SK-N-SH_RA	brain:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:19772686-19772736	T-47D	breast:	n/a
2	chr19:19772686-19772736	NH-A	brain:	n/a
3	chr19:19772686-19772736	Hela-S3	cervix:	n/a
4	chr19:19772686-19772736	MCF10A-Er-Src	breast:	n/a
5	chr19:19772686-19772736	AG09309	skin:	n/a
6	chr19:19772686-19772736	GM12891	blood:	n/a
7	chr19:19772686-19772736	BJ	skin:	n/a
8	chr19:19772686-19772736	SAEC	small airway:	n/a
9	chr19:19772686-19772736	HRCEpiC	kidney:	n/a
10	chr19:19772686-19772736	HEK293	kidney:	embryo
11	chr19:19772686-19772736	RPTEC	kidney:	n/a
12	chr19:19772686-19772736	GM06990	blood:	n/a
13	chr19:19772686-19772736	Jurkat	blood:	n/a
14	chr19:19772686-19772736	IMR90	lung:	fetal
15	chr19:19772686-19772736	K562	blood:	n/a
16	chr19:19772686-19772736	U87	brain:	n/a
17	chr19:19772686-19772736	CMK	blood:	n/a
18	chr19:19772686-19772736	A549	lung:	n/a
19	chr19:19772686-19772736	Hepatocyte	liver:	n/a
20	chr19:19772686-19772736	HUVEC	blood vessel:	n/a
21	chr19:19772686-19772736	SK-N-SH	brain:	n/a
22	chr19:19772686-19772736	SKMC	muscle:	n/a
23	chr19:19772686-19772736	PrEC	prostate:	n/a
24	chr19:19772686-19772736	AG04450	lung:	fetal
25	chr19:19772686-19772736	ProgFib	skin:	n/a
26	chr19:19772686-19772736	GM12878	blood:	n/a
27	chr19:19772686-19772736	NHDF-neo	bronchial:	n/a
28	chr19:19772686-19772736	NT2-D1	testis:	n/a
29	chr19:19772686-19772736	HAEpiC	amniotic membrane:	n/a
30	chr19:19772686-19772736	ECC-1	luminal epithelium:	n/a
31	chr19:19772686-19772736	MCF-7	breast:	n/a
32	chr19:19772686-19772736	HRE	kidney:	n/a
33	chr19:19772686-19772736	HPAEpiC	pulmonary alveolar:	n/a
34	chr19:19772686-19772736	Caco-2	colon:	n/a
35	chr19:19772686-19772736	PFSK-1	brain:	n/a
36	chr19:19772686-19772736	HRPEpiC	eye:	n/a
37	chr19:19772686-19772736	HNPCEpiC	eye:	n/a
38	chr19:19772686-19772736	SK-N-MC	brain:	n/a
39	chr19:19772686-19772736	AG10803	skin:	n/a
40	chr19:19772686-19772736	GM19239	blood:	n/a
41	chr19:19772686-19772736	BE2_C	brain:	n/a
42	chr19:19772686-19772736	HCT-116	colon:	n/a
43	chr19:19772686-19772736	PANC-1	pancreas:	n/a
44	chr19:19772686-19772736	HCM	heart:	n/a
45	chr19:19772686-19772736	HIPEpiC	eye:	n/a
46	chr19:19772686-19772736	SK-N-SH_RA	brain:	n/a
47	chr19:19772686-19772736	LNCaP	prostate:	n/a
48	chr19:19772686-19772736	ovcar-3	ovarian:	n/a
49	chr19:19772686-19772736	HL-60	blood:	n/a
50	chr19:19772686-19772736	HepG2	liver:	n/a

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19755704..19761642-chr19:19771468..19774473,6	MCF-7	breast:
2	chr19:19753534..19755355-chr19:19771479..19774786,3	MCF-7	breast:
3	chr19:19623259..19625867-chr19:19772617..19774685,2	MCF-7	breast:
4	chr19:19636166..19641062-chr19:19772143..19775843,4	MCF-7	breast:
5	chr19:19751259..19757786-chr19:19771999..19776232,8	K562	blood:
6	chr19:19649331..19652417-chr19:19771491..19776120,6	K562	blood:
7	chr19:19729417..19731495-chr19:19772370..19774542,2	MCF-7	breast:
8	chr19:19767560..19771032-chr19:19771876..19774701,8	MCF-7	breast:
9	chr19:19649600..19655493-chr19:19770960..19774805,7	K562	blood:
10	chr19:19751259..19758144-chr19:19770384..19776332,14	K562	blood:
11	chr19:19772600..19774395-chr19:19886060..19888388,2	MCF-7	breast:
12	chr19:19673046..19675875-chr19:19772243..19774932,2	K562	blood:
13	chr19:19772622..19775616-chr19:19842700..19844547,2	MCF-7	breast:
14	chr19:19753961..19756109-chr19:19770427..19773007,2	MCF-7	breast:
15	chr19:19772164..19776257-chr19:19777737..19781997,10	MCF-7	breast:

No data

Variant related genes	Relation type
ATP13A1	TF binding region
ATP13A1	CpG island
ENSG00000181896	Chromatin interaction
ENSG00000105708	Chromatin interaction
ENSG00000266904	Chromatin interaction
ENSG00000178093	Chromatin interaction
ENSG00000160161	Chromatin interaction
ENSG00000089639	Chromatin interaction
ENSG00000105726	Chromatin interaction
ENSG00000105717	Chromatin interaction
ENSG00000267419	Chromatin interaction
ENSG00000250067	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 11 )

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

rs_ID	r²[population]
rs10401926	0.88[CEU][hapmap]
rs10403579	0.80[EUR][1000 genomes]
rs10415278	0.88[CEU][hapmap]
rs10421328	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10423449	0.88[CEU][hapmap]
rs11667828	0.89[CEU][hapmap];0.81[TSI][hapmap]
rs11668721	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs11670710	0.89[CEU][hapmap];0.81[TSI][hapmap]
rs12983292	0.89[CEU][hapmap];0.81[TSI][hapmap]
rs2288867	0.82[CEU][hapmap]
rs55831814	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59327775	1.00[ASN][1000 genomes]
rs60030397	1.00[ASN][1000 genomes]
rs61752462	1.00[ASN][1000 genomes]
rs7253821	0.82[CEU][hapmap]
rs73006705	0.80[EUR][1000 genomes]
rs867616	0.88[CEU][hapmap]
rs884480	0.88[CEU][hapmap];0.85[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv911309	chr19:19727042-19784891	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv911310	chr19:19753882-19784891	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
5	esv3330851	chr19:19755507-19852881	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs919778	ZNF14	cis	cerebellum	SCAN
rs919778	MED26	cis	parietal	SCAN
rs919778	SNORA68	cis	parietal	SCAN
rs919778	BST2	cis	parietal	SCAN
rs919778	FKBP8	cis	parietal	SCAN
rs919778	C21orf128	trans	cerebellum	SCAN
rs919778	UNC13A	cis	cerebellum	SCAN
rs919778	ZNF14	cis	parietal	SCAN
rs919778	GMIP	cis	parietal	SCAN
rs919778	C19orf60	cis	parietal	SCAN
rs919778	EDG4	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19755400-19772800	Strong transcription	Thymus	Thymus
2	chr19:19766400-19772800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr19:19767000-19773400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr19:19768200-19773000	Weak transcription	Psoas Muscle	Psoas
5	chr19:19769600-19772800	Weak transcription	NH-A	brain
6	chr19:19769800-19773200	Weak transcription	Fetal Kidney	kidney
7	chr19:19770200-19772800	Weak transcription	HSMM	muscle
8	chr19:19770200-19773600	Weak transcription	Aorta	Aorta
9	chr19:19770600-19772800	Weak transcription	HSMMtube	muscle
10	chr19:19770800-19773000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr19:19770800-19773000	Weak transcription	Fetal Intestine Large	intestine
12	chr19:19770800-19773200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:19771200-19773000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr19:19771200-19773200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr19:19771200-19773200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr19:19771200-19773200	Weak transcription	Ovary	ovary
17	chr19:19771800-19772800	Enhancers	Primary B cells from cord blood	blood
18	chr19:19771800-19773000	Genic enhancers	Brain Cingulate Gyrus	brain
19	chr19:19772000-19772800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr19:19772000-19772800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr19:19772000-19772800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr19:19772000-19772800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr19:19772000-19772800	Genic enhancers	Lung	lung
24	chr19:19772000-19772800	Genic enhancers	K562	blood
25	chr19:19772000-19773000	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr19:19772000-19773000	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr19:19772000-19773000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr19:19772000-19773000	Enhancers	Muscle Satellite Cultured Cells	--
29	chr19:19772000-19773000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr19:19772000-19773000	Enhancers	Liver	Liver
31	chr19:19772000-19773000	Genic enhancers	Brain Germinal Matrix	brain
32	chr19:19772000-19773000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
33	chr19:19772000-19773200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr19:19772000-19773200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr19:19772000-19773200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr19:19772000-19773200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr19:19772000-19773200	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr19:19772000-19773200	Genic enhancers	Fetal Muscle Trunk	muscle
39	chr19:19772000-19773200	Genic enhancers	Gastric	stomach
40	chr19:19772000-19773200	Enhancers	Pancreas	Pancrea
41	chr19:19772000-19773200	Enhancers	Right Ventricle	heart
42	chr19:19772000-19773200	Enhancers	Stomach Mucosa	stomach
43	chr19:19772000-19773400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr19:19772000-19773400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr19:19772000-19773400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr19:19772000-19773400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr19:19772000-19773400	Enhancers	Fetal Brain Male	brain
48	chr19:19772000-19773400	Genic enhancers	Fetal Muscle Leg	muscle
49	chr19:19772000-19773600	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
50	chr19:19772000-19773600	Enhancers	Esophagus	oesophagus

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