Variant report

Variant	rs556512800
Chromosome Location	chr19:45311573-45311574
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	NR2F2	chr19:45311029-45312611	MCF-7	breast:	n/a	n/a
2	CTCF	chr19:45311151-45311601	K562	blood:	n/a	chr19:45311365-45311386 chr19:45311370-45311388 chr19:45311371-45311387
3	SP1	chr19:45311002-45312446	A549	lung:	n/a	chr19:45311679-45311688 chr19:45311467-45311481 chr19:45311678-45311692 chr19:45311331-45311345 chr19:45311466-45311478 chr19:45311678-45311688 chr19:45311466-45311478
4	RAD21	chr19:45311095-45311637	A549	lung:	n/a	chr19:45311368-45311387 chr19:45311378-45311385
5	TCF12	chr19:45311029-45312613	ECC-1	luminal epithelium:	n/a	chr19:45311761-45311769
6	MYBL2	chr19:45310990-45311616	HepG2	liver:	n/a	n/a
7	MAZ	chr19:45311056-45313023	IMR90	lung:	n/a	chr19:45311331-45311341
8	SMC3	chr19:45310944-45312433	SK-N-SH	brain:	n/a	chr19:45311372-45311386
9	SIN3AK20	chr19:45311152-45311847	A549	lung:	n/a	n/a
10	YY1	chr19:45311306-45311912	H1-hESC	embryonic stem cell:	n/a	n/a
11	STAT3	chr19:45311369-45311665	MCF10A-Er-Src	breast:	n/a	chr19:45311537-45311549 chr19:45311536-45311548 chr19:45311448-45311459
12	CHD2	chr19:45311191-45312492	H1-hESC	embryonic stem cell:	n/a	n/a
13	SIN3AK20	chr19:45311099-45312581	MCF-7	breast:	n/a	n/a
14	CTCF	chr19:45311080-45311648	MCF-7	breast:	n/a	chr19:45311365-45311386 chr19:45311370-45311388 chr19:45311371-45311387
15	ESR1	chr19:45311046-45311808	ECC-1	luminal epithelium:	n/a	n/a
16	CTCF	chr19:45311046-45311684	K562	blood:	n/a	chr19:45311365-45311386 chr19:45311370-45311388 chr19:45311371-45311387
17	POLR2A	chr19:45311270-45312616	ECC-1	luminal epithelium:	n/a	n/a
18	RAD21	chr19:45311119-45311666	MCF-7	breast:	n/a	chr19:45311368-45311387 chr19:45311378-45311385
19	ZBTB7A	chr19:45311182-45311626	HepG2	liver:	n/a	chr19:45311326-45311337
20	ZBTB7A	chr19:45311017-45313039	ECC-1	luminal epithelium:	n/a	chr19:45311326-45311337
21	TBP	chr19:45311259-45312590	H1-hESC	embryonic stem cell:	n/a	n/a
22	MAX	chr19:45311076-45312700	A549	lung:	n/a	chr19:45311331-45311341
23	ESR1	chr19:45311316-45311785	ECC-1	luminal epithelium:	n/a	n/a
24	EP300	chr19:45310984-45312779	ECC-1	luminal epithelium:	n/a	chr19:45312367-45312376
25	RAD21	chr19:45311164-45311655	H1-hESC	embryonic stem cell:	n/a	chr19:45311368-45311387 chr19:45311378-45311385
26	NR2F2	chr19:45311119-45312336	MCF-7	breast:	n/a	n/a
27	ATF2	chr19:45311188-45311983	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr19:45311238-45311730	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr19:45311180-45311587	MCF10A-Er-Src	breast:	n/a	n/a
30	RAD21	chr19:45311114-45311597	HepG2	liver:	n/a	chr19:45311368-45311387 chr19:45311378-45311385
31	CTCF	chr19:45311540-45311690	GM12865	blood:	n/a	n/a
32	YY1	chr19:45311211-45312129	H1-hESC	embryonic stem cell:	n/a	chr19:45312001-45312015
33	YY1	chr19:45311515-45311648	HCT-116	colon:	n/a	n/a
34	RAD21	chr19:45311147-45311627	MCF-7	breast:	n/a	chr19:45311368-45311387 chr19:45311378-45311385
35	CEBPD	chr19:45311160-45311701	HepG2	liver:	n/a	n/a
36	GATA3	chr19:45311385-45311877	T-47D	breast:	n/a	n/a
37	JUND	chr19:45311229-45311843	H1-hESC	embryonic stem cell:	n/a	n/a
38	NFIC	chr19:45311253-45312621	ECC-1	luminal epithelium:	n/a	n/a
39	CTCF	chr19:45310852-45312815	A549	lung:	n/a	chr19:45311365-45311386 chr19:45311370-45311388 chr19:45311371-45311387
40	SP1	chr19:45311135-45311922	H1-hESC	embryonic stem cell:	n/a	chr19:45311679-45311688 chr19:45311467-45311481 chr19:45311678-45311692 chr19:45311331-45311345 chr19:45311466-45311478 chr19:45311678-45311688 chr19:45311466-45311478
41	POLR2A	chr19:45311331-45312155	MCF10A-Er-Src	breast:	n/a	n/a
42	CTCF	chr19:45311520-45311670	GM12865	blood:	n/a	n/a
43	ZNF143	chr19:45311234-45311601	H1-hESC	embryonic stem cell:	n/a	chr19:45311438-45311457
44	MAX	chr19:45311206-45311810	H1-hESC	embryonic stem cell:	n/a	chr19:45311331-45311341
45	MYBL2	chr19:45311048-45311709	HepG2	liver:	n/a	n/a
46	MAX	chr19:45311180-45311829	MCF-7	breast:	n/a	chr19:45311331-45311341
47	POLR2A	chr19:45311188-45312660	HCT-116	colon:	n/a	n/a
48	POLR2A	chr19:45311062-45312807	H1-hESC	embryonic stem cell:	n/a	n/a
49	CTCF	chr19:45311520-45311670	HFF	foreskin:	n/a	n/a
50	MAX	chr19:45311159-45312450	ECC-1	luminal epithelium:	n/a	chr19:45311331-45311341

No.	Distal block	Cell Line	Cell type
1	chr19:45258326..45260627-chr19:45310152..45311875,2	MCF-7	breast:
2	chr19:45250785..45254453-chr19:45309921..45313662,4	MCF-7	breast:
3	chr19:45287462..45288194-chr19:45311126..45311751,2	MCF-7	breast:
4	chr19:45227043..45229115-chr19:45309849..45311993,3	MCF-7	breast:
5	chr19:45308884..45313334-chr19:45345353..45351688,18	MCF-7	breast:
6	chr19:45256385..45258826-chr19:45310390..45312154,2	MCF-7	breast:
7	chr19:45305840..45308889-chr19:45308989..45312130,4	MCF-7	breast:
8	chr19:45309744..45311644-chr19:45324913..45327057,2	MCF-7	breast:
9	chr19:45309587..45312322-chr19:45456957..45459370,2	MCF-7	breast:
10	chr19:45147379..45150123-chr19:45308817..45312008,3	MCF-7	breast:
11	chr19:45310566..45312166-chr19:45318337..45320547,2	K562	blood:
12	chr19:45298818..45303552-chr19:45309335..45312129,4	MCF-7	breast:
13	chr19:45308022..45312966-chr19:45346579..45352259,11	MCF-7	breast:
14	chr19:45249129..45253567-chr19:45309146..45313529,6	MCF-7	breast:
15	chr19:45311083..45313001-chr19:45347399..45349440,2	K562	blood:

Variant related genes	Relation type
BCAM	TF binding region
ENSG00000267114	Chromatin interaction
ENSG00000104853	Chromatin interaction
ENSG00000130202	Chromatin interaction
ENSG00000069399	Chromatin interaction
ENSG00000073008	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912117	chr19:45298069-45322744	Weak transcription Bivalent Enhancer ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
2	nsv912118	chr19:45300056-45326664	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv912119	chr19:45304307-45317089	Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv912120	chr19:45304307-45317469	Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
5	nsv912121	chr19:45304307-45319297	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv912122	chr19:45304307-45324516	Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv579861	chr19:45309972-45314395	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv912123	chr19:45310319-45314395	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
9	nsv579862	chr19:45310319-45316807	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
10	nsv912124	chr19:45310319-45318564	Enhancers Bivalent Enhancer Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
11	nsv912125	chr19:45310319-45321841	Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
12	nsv579863	chr19:45310319-45322451	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
13	nsv912126	chr19:45311523-45317089	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:45294200-45311600	Weak transcription	Small Intestine	intestine
2	chr19:45297000-45311800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr19:45309400-45311800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr19:45309600-45311800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr19:45309600-45311800	Enhancers	Placenta	Placenta
6	chr19:45309600-45311800	Enhancers	HMEC	breast
7	chr19:45309600-45311800	Enhancers	NHEK	skin
8	chr19:45309800-45312000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr19:45310000-45311600	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr19:45310200-45311800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr19:45310200-45311800	Enhancers	Fetal Intestine Large	intestine
12	chr19:45310200-45311800	Enhancers	Fetal Intestine Small	intestine
13	chr19:45310200-45311800	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr19:45310200-45312000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr19:45310200-45312400	Enhancers	Gastric	stomach
16	chr19:45310400-45311600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr19:45310400-45311600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr19:45310400-45311600	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr19:45310400-45311800	Enhancers	Fetal Muscle Trunk	muscle
20	chr19:45310400-45311800	Enhancers	Pancreas	Pancrea
21	chr19:45310400-45311800	Enhancers	Rectal Mucosa Donor 29	rectum
22	chr19:45310400-45312000	Enhancers	Stomach Mucosa	stomach
23	chr19:45310400-45312200	Flanking Active TSS	A549	lung
24	chr19:45310400-45312400	Enhancers	Esophagus	oesophagus
25	chr19:45310600-45311600	Enhancers	H1 Cell Line	embryonic stem cell
26	chr19:45310600-45311800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr19:45310600-45311800	Enhancers	Colonic Mucosa	Colon
28	chr19:45310600-45311800	Enhancers	Fetal Muscle Leg	muscle
29	chr19:45310600-45311800	Enhancers	Fetal Stomach	stomach
30	chr19:45310600-45311800	Enhancers	HSMMtube	muscle
31	chr19:45310800-45311600	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr19:45310800-45311600	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr19:45310800-45311800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr19:45310800-45311800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr19:45310800-45311800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr19:45311000-45311800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr19:45311000-45311800	Enhancers	Muscle Satellite Cultured Cells	--
38	chr19:45311000-45311800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr19:45311000-45312000	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr19:45311000-45312000	Enhancers	Brain Angular Gyrus	brain
41	chr19:45311200-45311600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr19:45311200-45311600	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr19:45311200-45311600	Flanking Active TSS	Hela-S3	cervix
44	chr19:45311200-45311800	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr19:45311200-45311800	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr19:45311200-45311800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr19:45311200-45311800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr19:45311200-45311800	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr19:45311200-45311800	Enhancers	Colon Smooth Muscle	Colon
50	chr19:45311200-45311800	Enhancers	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links