Variant report

Variant	rs562159656
Chromosome Location	chr19:18058137-18058138
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	HCFC1	chr19:18058050-18059886	Hela-S3	cervix:	n/a	n/a
2	TAF1	chr19:18058053-18058911	H1-hESC	embryonic stem cell:	n/a	n/a
3	GTF2F1	chr19:18058127-18058327	Hela-S3	cervix:	n/a	n/a
4	SRF	chr19:18058037-18058419	GM12878	blood:	n/a	chr19:18058236-18058245 chr19:18058234-18058245 chr19:18058233-18058248 chr19:18058236-18058247 chr19:18058234-18058247 chr19:18058230-18058248 chr19:18058235-18058246
5	ELK1	chr19:18058063-18058775	GM12878	blood:	n/a	n/a
6	SRF	chr19:18058108-18058514	ECC-1	luminal epithelium:	n/a	chr19:18058236-18058245 chr19:18058234-18058245 chr19:18058233-18058248 chr19:18058236-18058247 chr19:18058234-18058247 chr19:18058230-18058248 chr19:18058235-18058246
7	SRF	chr19:18058122-18058409	GM12878	blood:	n/a	chr19:18058236-18058245 chr19:18058234-18058245 chr19:18058233-18058248 chr19:18058236-18058247 chr19:18058234-18058247 chr19:18058230-18058248 chr19:18058235-18058246
8	SRF	chr19:18057954-18058442	H1-hESC	embryonic stem cell:	n/a	chr19:18058236-18058245 chr19:18058234-18058245 chr19:18058233-18058248 chr19:18058236-18058247 chr19:18058234-18058247 chr19:18058230-18058248 chr19:18058235-18058246
9	POLR2A	chr19:18057887-18058638	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr19:18058031-18058904	MCF10A-Er-Src	breast:	n/a	n/a
11	SRF	chr19:18058055-18058499	ECC-1	luminal epithelium:	n/a	chr19:18058236-18058245 chr19:18058234-18058245 chr19:18058233-18058248 chr19:18058236-18058247 chr19:18058234-18058247 chr19:18058230-18058248 chr19:18058235-18058246
12	EGR1	chr19:18057935-18059457	HCT-116	colon:	n/a	chr19:18058919-18058929 chr19:18058714-18058728 chr19:18059037-18059047 chr19:18059038-18059051 chr19:18058920-18058930 chr19:18058982-18058995 chr19:18058926-18058936 chr19:18058987-18058997 chr19:18058893-18058902 chr19:18059168-18059177 chr19:18058712-18058727 chr19:18058666-18058675 chr19:18058813-18058822 chr19:18058921-18058934 chr19:18058928-18058941 chr19:18058737-18058746
13	MXI1	chr19:18057929-18059514	SK-N-SH	brain:	n/a	n/a
14	SRF	chr19:18058013-18058916	MCF-7	breast:	n/a	chr19:18058236-18058245 chr19:18058234-18058245 chr19:18058233-18058248 chr19:18058751-18058761 chr19:18058236-18058247 chr19:18058234-18058247 chr19:18058230-18058248 chr19:18058235-18058246
15	POLR2A	chr19:18058095-18058744	GM12878	blood:	n/a	n/a
16	POLR2A	chr19:18058048-18058594	H1-hESC	embryonic stem cell:	n/a	n/a
17	SRF	chr19:18057988-18058504	H1-hESC	embryonic stem cell:	n/a	chr19:18058236-18058245 chr19:18058234-18058245 chr19:18058233-18058248 chr19:18058236-18058247 chr19:18058234-18058247 chr19:18058230-18058248 chr19:18058235-18058246
18	NRF1	chr19:18058129-18059456	SK-N-SH	brain:	n/a	chr19:18058920-18058929 chr19:18059169-18059178 chr19:18058665-18058679 chr19:18059167-18059181 chr19:18058889-18058903 chr19:18059164-18059178 chr19:18058927-18058936 chr19:18058814-18058823 chr19:18058809-18058823 chr19:18058667-18058676 chr19:18059167-18059178 chr19:18058812-18058826 chr19:18058892-18058901 chr19:18058665-18058676 chr19:18058812-18058823 chr19:18058812-18058823 chr19:18058838-18058849 chr19:18058987-18058996 chr19:18058892-18058903
19	ELK1	chr19:18058094-18058529	K562	blood:	n/a	n/a
20	POLR2A	chr19:18057865-18060070	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr19:18058118-18058886	K562	blood:	n/a	n/a
22	POLR2A	chr19:18057979-18058945	K562	blood:	n/a	n/a
23	TAF1	chr19:18058054-18058601	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr19:18058037-18058688	H1-hESC	embryonic stem cell:	n/a	n/a
25	USF1	chr19:18058112-18058279	HepG2	liver:	n/a	chr19:18058226-18058237
26	TAF7	chr19:18058108-18058645	H1-hESC	embryonic stem cell:	n/a	n/a
27	USF1	chr19:18058002-18058385	H1-hESC	embryonic stem cell:	n/a	chr19:18058226-18058237
28	MXI1	chr19:18058006-18059362	IMR90	lung:	n/a	n/a
29	RUNX3	chr19:18058017-18059276	GM12878	blood:	n/a	n/a
30	SRF	chr19:18058086-18058337	K562	blood:	n/a	chr19:18058236-18058245 chr19:18058234-18058245 chr19:18058233-18058248 chr19:18058236-18058247 chr19:18058234-18058247 chr19:18058230-18058248 chr19:18058235-18058246
31	SRF	chr19:18058091-18058320	HepG2	liver:	n/a	chr19:18058236-18058245 chr19:18058234-18058245 chr19:18058233-18058248 chr19:18058236-18058247 chr19:18058234-18058247 chr19:18058230-18058248 chr19:18058235-18058246
32	SRF	chr19:18057931-18058666	MCF-7	breast:	n/a	chr19:18058236-18058245 chr19:18058234-18058245 chr19:18058233-18058248 chr19:18058236-18058247 chr19:18058234-18058247 chr19:18058230-18058248 chr19:18058235-18058246
33	MXI1	chr19:18058003-18058256	Hela-S3	cervix:	n/a	n/a
34	CTCF	chr19:18058120-18058270	HMEC	breast:	n/a	n/a
35	RUNX3	chr19:18058083-18058443	GM12878	blood:	n/a	n/a
36	USF1	chr19:18058048-18058374	H1-hESC	embryonic stem cell:	n/a	chr19:18058226-18058237
37	POLR2A	chr19:18058081-18058604	H1-hESC	embryonic stem cell:	n/a	n/a
38	SRF	chr19:18058126-18058360	GM12878	blood:	n/a	chr19:18058236-18058245 chr19:18058234-18058245 chr19:18058233-18058248 chr19:18058236-18058247 chr19:18058234-18058247 chr19:18058230-18058248 chr19:18058235-18058246
39	SIN3AK20	chr19:18058093-18059308	MCF-7	breast:	n/a	n/a
40	MAZ	chr19:18058106-18059666	IMR90	lung:	n/a	chr19:18059607-18059617 chr19:18058439-18058448
41	STAT5A	chr19:18058123-18058572	GM12878	blood:	n/a	n/a
42	MTA3	chr19:18058058-18058742	GM12878	blood:	n/a	n/a
43	STAT1	chr19:18058111-18058403	GM12878	blood:	n/a	n/a
44	CUX1	chr19:18058097-18058418	K562	blood:	n/a	chr19:18058287-18058296
45	SRF	chr19:18058102-18058447	GM12878	blood:	n/a	chr19:18058236-18058245 chr19:18058234-18058245 chr19:18058233-18058248 chr19:18058236-18058247 chr19:18058234-18058247 chr19:18058230-18058248 chr19:18058235-18058246
46	POLR2A	chr19:18058088-18059210	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr19:18058113-18058723	GM12892	blood:	n/a	n/a
48	POLR2A	chr19:18058056-18058922	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:18049354..18052020-chr19:18056652..18058961,3	MCF-7	breast:
2	chr19:18057229..18058563-chr19:18107268..18108242,5	MCF-7	breast:
3	chr19:18056861..18058558-chr19:18107372..18108294,7	K562	blood:
4	chr19:17984874..17987363-chr19:18056604..18058812,2	K562	blood:
5	chr19:18057024..18060346-chr19:18095045..18097691,3	K562	blood:
6	chr19:18056470..18058244-chr19:18107377..18108277,8	MCF-7	breast:
7	chr19:18055988..18065489-chr19:18073307..18083163,16	K562	blood:
8	chr19:18057399..18062095-chr19:18108081..18112546,5	K562	blood:
9	chr19:18057353..18059947-chr19:18110814..18113485,3	MCF-7	breast:
10	chr19:18057965..18060030-chr19:18157844..18159639,2	K562	blood:
11	chr19:18052069..18059812-chr19:18106129..18113779,16	K562	blood:
12	chr19:17974807..17978167-chr19:18058036..18060976,4	K562	blood:
13	chr19:18057341..18060009-chr19:18227603..18230383,4	K562	blood:
14	chr19:17969435..17972591-chr19:18056494..18062279,6	K562	blood:
15	chr19:18057090..18059767-chr19:18110634..18113948,3	MCF-7	breast:
16	chr19:17969156..17972643-chr19:18057294..18060299,6	K562	blood:

Variant related genes	Relation type
KCNN1	TF binding region
ENSG00000252591	Chromatin interaction
ENSG00000105640	Chromatin interaction
ENSG00000105642	Chromatin interaction
ENSG00000243455	Chromatin interaction
ENSG00000105643	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911214	chr19:17827442-18123965	Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
2	nsv1055932	chr19:17923918-18369944	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
3	nsv543923	chr19:17923918-18369944	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv833772	chr19:17965173-18139337	Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
5	nsv911226	chr19:18007077-18075077	Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv911227	chr19:18007077-18117646	Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv532614	chr19:18033043-18573963	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	204 gene(s)	inside rSNPs	diseases
8	nsv911228	chr19:18038782-18101830	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv911229	chr19:18042945-18117646	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
10	nsv470130	chr19:18047283-18234587	Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
11	esv3406796	chr19:18057477-18060725	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
12	esv3358201	chr19:18058077-18060550	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18044600-18058200	Weak transcription	Psoas Muscle	Psoas
2	chr19:18044800-18058200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:18047800-18058200	Weak transcription	Left Ventricle	heart
4	chr19:18051200-18058200	Weak transcription	Aorta	Aorta
5	chr19:18054200-18058200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:18054800-18058200	Weak transcription	Fetal Lung	lung
7	chr19:18055000-18058200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr19:18055000-18058200	Weak transcription	Right Ventricle	heart
9	chr19:18055200-18058200	Weak transcription	Ovary	ovary
10	chr19:18055200-18058200	Weak transcription	HSMM	muscle
11	chr19:18055400-18058200	Weak transcription	Gastric	stomach
12	chr19:18055600-18058200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr19:18055600-18058200	Weak transcription	HSMMtube	muscle
14	chr19:18055600-18058200	Weak transcription	NHLF	lung
15	chr19:18055800-18058200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr19:18056000-18058200	Weak transcription	Esophagus	oesophagus
17	chr19:18056800-18058200	Enhancers	Primary B cells from peripheral blood	blood
18	chr19:18057200-18058200	Enhancers	Fetal Thymus	thymus
19	chr19:18057800-18058200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr19:18057800-18058200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr19:18057800-18058200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr19:18057800-18058200	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr19:18057800-18058200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr19:18057800-18058200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr19:18057800-18058200	Enhancers	Placenta	Placenta
26	chr19:18057800-18058400	Enhancers	Spleen	Spleen
27	chr19:18057800-18058400	Flanking Active TSS	GM12878-XiMat	blood
28	chr19:18057800-18058600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
29	chr19:18057800-18058600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr19:18058000-18058200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
31	chr19:18058000-18058200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr19:18058000-18058200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr19:18058000-18058200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr19:18058000-18058200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr19:18058000-18058200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr19:18058000-18058200	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr19:18058000-18058200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr19:18058000-18058200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
39	chr19:18058000-18058200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
40	chr19:18058000-18058200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr19:18058000-18058200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr19:18058000-18058200	Enhancers	Muscle Satellite Cultured Cells	--
43	chr19:18058000-18058200	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr19:18058000-18058200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr19:18058000-18058200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr19:18058000-18058200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr19:18058000-18058200	Enhancers	Liver	Liver
48	chr19:18058000-18058200	Enhancers	Brain Germinal Matrix	brain
49	chr19:18058000-18058200	Enhancers	Duodenum Mucosa	Duodenum
50	chr19:18058000-18058200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum

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