Variant report

Variant	rs556096340
Chromosome Location	chr19:39138205-39138206
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	TBP	chr19:39137834-39138504	HepG2	liver:	n/a	n/a
2	ETS1	chr19:39138150-39138681	K562	blood:	n/a	n/a
3	NANOG	chr19:39137909-39138464	H1-hESC	embryonic stem cell:	n/a	n/a
4	SIN3AK20	chr19:39137730-39142454	PANC-1	pancreas:	n/a	n/a
5	TAF1	chr19:39137878-39138737	ECC-1	luminal epithelium:	n/a	n/a
6	BCL3	chr19:39137727-39141534	A549	lung:	n/a	chr19:39139820-39139833 chr19:39139573-39139582 chr19:39138040-39138049 chr19:39139822-39139831
7	POLR2A	chr19:39137959-39138558	GM10847	blood:	n/a	n/a
8	YY1	chr19:39137918-39138535	SK-N-SH_RA	brain:	n/a	n/a
9	POLR2A	chr19:39137823-39138741	GM12892	blood:	n/a	n/a
10	SP1	chr19:39137830-39138554	GM12878	blood:	n/a	chr19:39138058-39138070 chr19:39138059-39138069 chr19:39138059-39138068 chr19:39138058-39138070 chr19:39138060-39138069
11	TAF1	chr19:39137806-39138671	MCF-7	breast:	n/a	n/a
12	CTCF	chr19:39138162-39138246	Lung_OC	lung:	n/a	n/a
13	POLR2A	chr19:39137848-39138578	GM18526	blood:	n/a	n/a
14	POU2F2	chr19:39137835-39138508	GM12878	blood:	n/a	chr19:39138093-39138105
15	MAX	chr19:39138065-39138589	K562	blood:	n/a	n/a
16	TAF1	chr19:39138106-39138607	H1-hESC	embryonic stem cell:	n/a	n/a
17	TAF1	chr19:39138141-39139117	H1-hESC	embryonic stem cell:	n/a	n/a
18	REST	chr19:39138170-39139027	A549	lung:	n/a	n/a
19	TAF1	chr19:39138084-39138521	PFSK-1	brain:	n/a	n/a
20	GATA3	chr19:39137683-39143576	A549	lung:	n/a	chr19:39142854-39142870 chr19:39141250-39141260 chr19:39139349-39139362 chr19:39140563-39140573 chr19:39143239-39143246 chr19:39142851-39142872 chr19:39140861-39140871
21	POLR2A	chr19:39137804-39138563	K562	blood:	n/a	n/a
22	E2F4	chr19:39137987-39138533	GM12878	blood:	n/a	chr19:39138101-39138110 chr19:39138213-39138224 chr19:39138025-39138035 chr19:39138153-39138162
23	E2F6	chr19:39137808-39139193	A549	lung:	n/a	chr19:39138101-39138110 chr19:39138025-39138035 chr19:39138153-39138162
24	TAF7	chr19:39138113-39138595	H1-hESC	embryonic stem cell:	n/a	n/a
25	PBX3	chr19:39137752-39141451	A549	lung:	n/a	n/a
26	ATF3	chr19:39137815-39138663	A549	lung:	n/a	n/a
27	NR3C1	chr19:39137898-39138614	A549	lung:	n/a	n/a
28	FOSL2	chr19:39137753-39138607	SK-N-SH	brain:	n/a	n/a
29	SMC3	chr19:39137920-39138505	Hela-S3	cervix:	n/a	n/a
30	SIN3AK20	chr19:39138128-39138848	K562	blood:	n/a	n/a
31	FOXA1	chr19:39138064-39138490	HepG2	liver:	n/a	n/a
32	JUN	chr19:39137890-39138518	K562	blood:	n/a	n/a
33	ELF1	chr19:39137910-39138767	GM12878	blood:	n/a	n/a
34	ZBTB7A	chr19:39138175-39138646	ECC-1	luminal epithelium:	n/a	chr19:39138591-39138599
35	HA-E2F1	chr19:39137812-39138522	MCF-7	breast:	n/a	chr19:39138101-39138110 chr19:39138025-39138035 chr19:39138153-39138162 chr19:39138220-39138231
36	PAX5	chr19:39137884-39138405	GM12878	blood:	n/a	chr19:39138206-39138215 chr19:39138208-39138217
37	PBX3	chr19:39137761-39138704	SK-N-SH	brain:	n/a	n/a
38	RAD21	chr19:39137907-39138812	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr19:39138144-39138580	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr19:39137851-39138622	HCT-116	colon:	n/a	n/a
41	YY1	chr19:39137816-39138659	GM12892	blood:	n/a	n/a
42	CEBPD	chr19:39137947-39138577	HepG2	liver:	n/a	n/a
43	POU2F2	chr19:39137872-39138575	GM12891	blood:	n/a	chr19:39138093-39138105
44	TAF1	chr19:39138161-39138486	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr19:39137898-39139116	ECC-1	luminal epithelium:	n/a	n/a
46	ELF1	chr19:39137912-39138259	A549	lung:	n/a	n/a
47	TAF1	chr19:39138204-39138549	GM12891	blood:	n/a	n/a
48	MAX	chr19:39138105-39138653	H1-hESC	embryonic stem cell:	n/a	n/a
49	REST	chr19:39138120-39138559	HepG2	liver:	n/a	n/a
50	POLR2A	chr19:39137840-39141272	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39138022..39142840-chr19:39322070..39325450,5	MCF-7	breast:
2	chr12:49760885..49761567-chr19:39137909..39138667,2	HCT-116	colon:
3	chr19:39137328..39141053-chr19:39337803..39340723,6	MCF-7	breast:
4	chr19:39127732..39130687-chr19:39136486..39138250,3	MCF-7	breast:
5	chr19:39137520..39139996-chr19:39320132..39324117,5	MCF-7	breast:
6	chr19:39135966..39142009-chr19:39184894..39201240,23	MCF-7	breast:
7	chr19:39107241..39111219-chr19:39136508..39140596,7	K562	blood:
8	chr19:39137047..39143767-chr19:39341076..39344906,12	MCF-7	breast:
9	chr19:39137584..39140325-chr19:39327324..39331607,4	MCF-7	breast:
10	chr19:39108167..39112213-chr19:39136508..39140596,7	K562	blood:
11	chr10:99496914..99497435-chr19:39137923..39138480,2	NB4	blood:
12	chr19:39138189..39142372-chr19:39210085..39214804,5	MCF-7	breast:
13	chr19:39136334..39138370-chr19:39226702..39229509,2	MCF-7	breast:
14	chr19:39137231..39139589-chr19:39329369..39331157,2	MCF-7	breast:
15	chr19:39135827..39140696-chr19:39337712..39343036,10	MCF-7	breast:
16	chr19:39109034..39110948-chr19:39138125..39139962,2	MCF-7	breast:
17	chr19:39104481..39107303-chr19:39137807..39140302,2	K562	blood:
18	chr19:39138000..39140768-chr19:39215687..39223350,9	MCF-7	breast:

Variant related genes	Relation type
ACTN4	TF binding region
ENSG00000104823	Chromatin interaction
ENSG00000178982	Chromatin interaction
ENSG00000155256	Chromatin interaction
ENSG00000123352	Chromatin interaction
ENSG00000267892	Chromatin interaction
ENSG00000104814	Chromatin interaction
ENSG00000130402	Chromatin interaction
ENSG00000182472	Chromatin interaction
ENSG00000104824	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833826	chr19:38945106-39184547	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv833827	chr19:38993054-39184547	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv833828	chr19:39084759-39257979	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
6	nsv1057901	chr19:39112486-39174332	Genic enhancers Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
7	nsv911667	chr19:39119898-39143289	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
8	esv18193	chr19:39138183-39140365	Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39126600-39138400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr19:39127600-39138400	Weak transcription	Aorta	Aorta
3	chr19:39128400-39138400	Weak transcription	Primary T cells from cord blood	blood
4	chr19:39137000-39138400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr19:39137600-39138600	Active TSS	Primary neutrophils fromperipheralblood	blood
6	chr19:39137600-39139400	Active TSS	Skeletal Muscle Female	skeletal muscle
7	chr19:39137600-39139800	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr19:39137600-39140400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr19:39137800-39138400	Active TSS	Primary B cells from cord blood	blood
10	chr19:39137800-39138400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr19:39137800-39138400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr19:39137800-39138400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr19:39137800-39138400	Active TSS	HepG2	liver
14	chr19:39137800-39138600	Active TSS	Primary T helper cells fromperipheralblood	blood
15	chr19:39137800-39138600	Enhancers	Fetal Brain Male	brain
16	chr19:39137800-39138600	Active TSS	Thymus	Thymus
17	chr19:39137800-39138800	Active TSS	Monocytes-CD14+_RO01746	blood
18	chr19:39137800-39139000	Active TSS	Fetal Brain Female	brain
19	chr19:39137800-39139200	Active TSS	Brain Germinal Matrix	brain
20	chr19:39137800-39139200	Active TSS	Colon Smooth Muscle	Colon
21	chr19:39137800-39139400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr19:39137800-39139400	Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr19:39137800-39139400	Active TSS	Brain Anterior Caudate	brain
24	chr19:39137800-39139600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr19:39137800-39139600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr19:39137800-39139600	Active TSS	Colonic Mucosa	Colon
27	chr19:39137800-39139800	Active TSS	Fetal Muscle Leg	muscle
28	chr19:39137800-39139800	Active TSS	Fetal Stomach	stomach
29	chr19:39137800-39140000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:39137800-39140000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr19:39137800-39140000	Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr19:39137800-39140000	Active TSS	Brain Substantia Nigra	brain
33	chr19:39137800-39140000	Active TSS	Fetal Lung	lung
34	chr19:39137800-39140000	Active TSS	Placenta	Placenta
35	chr19:39137800-39140000	Active TSS	Stomach Smooth Muscle	stomach
36	chr19:39137800-39140000	Active TSS	GM12878-XiMat	blood
37	chr19:39137800-39140000	Active TSS	K562	blood
38	chr19:39137800-39140200	Active TSS	H1 Cell Line	embryonic stem cell
39	chr19:39137800-39140200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr19:39137800-39140200	Active TSS	Brain Angular Gyrus	brain
41	chr19:39137800-39140200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr19:39137800-39140200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
43	chr19:39137800-39140200	Active TSS	Ovary	ovary
44	chr19:39137800-39140200	Active TSS	Right Ventricle	heart
45	chr19:39137800-39140400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr19:39137800-39140600	Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr19:39137800-39140800	Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr19:39137800-39140800	Active TSS	Rectal Smooth Muscle	rectum
49	chr19:39137800-39140800	Active TSS	Sigmoid Colon	Sigmoid Colon
50	chr19:39137800-39140800	Active TSS	NH-A	brain

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