Variant report

Variant	rs555620558
Chromosome Location	chr19:18654232-18654233
allele	G/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	POLR2A	chr19:18654172-18654527	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr19:18653858-18655103	GM19099	blood:	n/a	n/a
3	SP1	chr19:18654159-18655155	H1-hESC	embryonic stem cell:	n/a	chr19:18654388-18654400 chr19:18654388-18654400 chr19:18654389-18654399 chr19:18654389-18654399 chr19:18654389-18654398 chr19:18654396-18654417 chr19:18654389-18654398 chr19:18654390-18654399
4	ZBTB7A	chr19:18653262-18655069	ECC-1	luminal epithelium:	n/a	n/a
5	ZBTB7A	chr19:18653457-18655062	K562	blood:	n/a	n/a
6	POLR2A	chr19:18654173-18654536	GM12878	blood:	n/a	n/a
7	SP1	chr19:18654161-18654725	A549	lung:	n/a	chr19:18654388-18654400 chr19:18654388-18654400 chr19:18654389-18654399 chr19:18654389-18654399 chr19:18654389-18654398 chr19:18654396-18654417 chr19:18654389-18654398 chr19:18654390-18654399
8	SP1	chr19:18654200-18655314	HCT-116	colon:	n/a	chr19:18654388-18654400 chr19:18654388-18654400 chr19:18654389-18654399 chr19:18654389-18654399 chr19:18654389-18654398 chr19:18654396-18654417 chr19:18654389-18654398 chr19:18654390-18654399
9	ELF1	chr19:18654213-18655130	GM12878	blood:	n/a	chr19:18654389-18654401 chr19:18654418-18654427
10	EGR1	chr19:18654104-18654453	K562	blood:	n/a	n/a
11	HDAC2	chr19:18654184-18654525	HepG2	liver:	n/a	n/a
12	POLR2A	chr19:18654211-18654399	A549	lung:	n/a	n/a
13	POLR2A	chr19:18654131-18654585	H1-neurons	neurons:	n/a	n/a
14	GABPA	chr19:18654201-18654691	SK-N-SH	brain:	n/a	n/a
15	ELF1	chr19:18654230-18654556	HepG2	liver:	n/a	chr19:18654389-18654401 chr19:18654418-18654427
16	POLR2A	chr19:18654166-18654534	H1-neurons	neurons:	n/a	n/a
17	POLR2A	chr19:18654166-18655216	K562	blood:	n/a	n/a
18	TCF12	chr19:18653756-18654545	ECC-1	luminal epithelium:	n/a	chr19:18653832-18653842
19	EGR1	chr19:18654117-18654407	GM12878	blood:	n/a	n/a
20	POLR2A	chr19:18654216-18655137	GM15510	blood:	n/a	n/a
21	SP1	chr19:18654154-18654678	A549	lung:	n/a	chr19:18654388-18654400 chr19:18654388-18654400 chr19:18654389-18654399 chr19:18654389-18654399 chr19:18654389-18654398 chr19:18654396-18654417 chr19:18654389-18654398 chr19:18654390-18654399
22	HCFC1	chr19:18654181-18655385	Hela-S3	cervix:	n/a	n/a
23	EGR1	chr19:18653775-18654525	K562	blood:	n/a	chr19:18653789-18653802 chr19:18653883-18653898 chr19:18653835-18653845
24	GABPA	chr19:18654188-18655144	K562	blood:	n/a	chr19:18654960-18654974 chr19:18654963-18654972
25	GABPA	chr19:18654204-18654573	MCF-7	breast:	n/a	n/a
26	POLR2A	chr19:18654181-18655209	SK-N-MC	brain:	n/a	n/a
27	CHD2	chr19:18654222-18655118	Hela-S3	cervix:	n/a	n/a
28	PBX3	chr19:18654147-18654752	SK-N-SH	brain:	n/a	chr19:18654441-18654461 chr19:18654406-18654415 chr19:18654410-18654430
29	CEBPD	chr19:18654164-18654632	HepG2	liver:	n/a	n/a
30	PBX3	chr19:18654135-18654593	SK-N-SH	brain:	n/a	chr19:18654441-18654461 chr19:18654406-18654415 chr19:18654410-18654430
31	SP1	chr19:18654150-18654672	GM12878	blood:	n/a	chr19:18654388-18654400 chr19:18654388-18654400 chr19:18654389-18654399 chr19:18654389-18654399 chr19:18654389-18654398 chr19:18654396-18654417 chr19:18654389-18654398 chr19:18654390-18654399
32	RUNX3	chr19:18654184-18654522	GM12878	blood:	n/a	n/a
33	POLR2A	chr19:18653461-18655322	K562	blood:	n/a	n/a
34	POLR2A	chr19:18654160-18655204	HepG2	liver:	n/a	n/a
35	SP1	chr19:18654137-18655115	H1-hESC	embryonic stem cell:	n/a	chr19:18654388-18654400 chr19:18654388-18654400 chr19:18654389-18654399 chr19:18654389-18654399 chr19:18654389-18654398 chr19:18654396-18654417 chr19:18654389-18654398 chr19:18654390-18654399
36	POLR2A	chr19:18654194-18654548	K562	blood:	n/a	n/a
37	CREB1	chr19:18653722-18655186	GM12878	blood:	n/a	n/a
38	MAX	chr19:18654205-18654523	K562	blood:	n/a	n/a
39	MAX	chr19:18654165-18655218	K562	blood:	n/a	n/a
40	SP2	chr19:18654188-18654531	H1-hESC	embryonic stem cell:	n/a	chr19:18654405-18654415 chr19:18654335-18654350 chr19:18654388-18654403 chr19:18654440-18654463
41	CREB1	chr19:18654184-18654531	A549	lung:	n/a	n/a
42	ELF1	chr19:18654199-18654680	K562	blood:	n/a	chr19:18654389-18654401 chr19:18654418-18654427
43	CHD2	chr19:18654203-18655183	GM12878	blood:	n/a	n/a
44	POLR2A	chr19:18654200-18654516	ECC-1	luminal epithelium:	n/a	n/a
45	SP2	chr19:18654203-18654561	K562	blood:	n/a	chr19:18654405-18654415 chr19:18654335-18654350 chr19:18654388-18654403 chr19:18654440-18654463
46	HEY1	chr19:18654183-18654516	HepG2	liver:	n/a	chr19:18654414-18654429
47	POLR2A	chr19:18654207-18655202	Raji	blood:	n/a	n/a
48	YY1	chr19:18654210-18654516	GM12878	blood:	n/a	chr19:18654415-18654426 chr19:18654412-18654426
49	PBX3	chr19:18654210-18654706	A549	lung:	n/a	chr19:18654441-18654461 chr19:18654406-18654415 chr19:18654410-18654430
50	POLR2A	chr19:18654213-18655142	GM18505	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:18651038..18656783-chr19:18680897..18685521,14	K562	blood:
2	chr19:18653032..18656930-chr19:18667045..18670995,8	MCF-7	breast:
3	chr19:18651498..18655648-chr19:18680777..18683781,5	MCF-7	breast:
4	chr19:18653590..18656982-chr19:18704077..18706738,3	K562	blood:
5	chr19:18536175..18537815-chr19:18653605..18655763,2	MCF-7	breast:
6	chr19:18648889..18650815-chr19:18652717..18655388,4	K562	blood:
7	chr19:18630875..18635401-chr19:18651200..18655863,9	MCF-7	breast:
8	chr19:18629748..18634724-chr19:18652806..18658264,15	K562	blood:
9	chr19:18653886..18656782-chr19:18668675..18670368,2	MCF-7	breast:
10	chr19:18652388..18655450-chr19:18667016..18670630,4	K562	blood:
11	chr19:18652388..18654838-chr19:18668474..18670630,2	K562	blood:
12	chr19:18629917..18634196-chr19:18652150..18655589,5	MCF-7	breast:
13	chr19:18653459..18656385-chr19:18699225..18703130,9	K562	blood:
14	chr19:18653470..18656783-chr19:18680897..18684291,6	K562	blood:
15	chr19:18653476..18656385-chr19:18700159..18703130,5	K562	blood:
16	chr19:18629959..18634840-chr19:18652830..18656407,13	K562	blood:

Variant related genes	Relation type
FKBP8	TF binding region
ENSG00000221983	Chromatin interaction
ENSG00000105656	Chromatin interaction
ENSG00000105701	Chromatin interaction
ENSG00000105700	Chromatin interaction
ENSG00000130511	Chromatin interaction
ENSG00000006015	Chromatin interaction
ENSG00000006016	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911274	chr19:18440942-18691942	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	nsv428018	chr19:18454891-18663981	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	61 gene(s)	inside rSNPs	diseases
5	nsv532615	chr19:18534867-18796031	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
6	nsv1061733	chr19:18574940-18679155	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
7	nsv1055794	chr19:18611545-18676933	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
8	nsv911281	chr19:18613917-18758255	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
9	nsv911282	chr19:18624964-18928480	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
10	nsv911283	chr19:18626732-18689830	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
11	nsv833776	chr19:18638028-18782264	Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
12	nsv911284	chr19:18643036-18684216	Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
13	nsv911285	chr19:18646932-18667472	Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	esv3345432	chr19:18652252-18655950	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
15	esv3446773	chr19:18652777-18655825	Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
16	nsv911286	chr19:18652844-18811112	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
17	esv3395824	chr19:18653052-18655650	Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
18	esv3339801	chr19:18653352-18655350	Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18632800-18654600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:18652600-18654600	Active TSS	Brain Angular Gyrus	brain
3	chr19:18652800-18654800	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr19:18652800-18654800	Active TSS	HSMM	muscle
5	chr19:18653000-18654600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr19:18653000-18654600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr19:18653000-18654800	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr19:18653000-18655000	Active TSS	H9 Cell Line	embryonic stem cell
9	chr19:18653000-18655000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr19:18653000-18655000	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr19:18653000-18655000	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr19:18653200-18654600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr19:18653200-18654600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr19:18653200-18654600	Active TSS	Ovary	ovary
15	chr19:18653200-18654600	Active TSS	NHDF-Ad	bronchial
16	chr19:18653200-18654800	Active TSS	H1 Cell Line	embryonic stem cell
17	chr19:18653200-18654800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr19:18653200-18654800	Active TSS	Esophagus	oesophagus
19	chr19:18653200-18654800	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr19:18653200-18654800	Active TSS	Lung	lung
21	chr19:18653200-18654800	Active TSS	Right Atrium	heart
22	chr19:18653200-18654800	Active TSS	HSMMtube	muscle
23	chr19:18653200-18655000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr19:18653400-18654600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr19:18653400-18654600	Active TSS	Brain Anterior Caudate	brain
26	chr19:18653400-18654600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr19:18653400-18654600	Active TSS	Brain Substantia Nigra	brain
28	chr19:18653400-18654600	Active TSS	NHLF	lung
29	chr19:18653400-18654800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:18653400-18654800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr19:18653400-18654800	Active TSS	Aorta	Aorta
32	chr19:18653400-18654800	Active TSS	Brain Germinal Matrix	brain
33	chr19:18653400-18654800	Active TSS	Fetal Brain Female	brain
34	chr19:18653400-18655000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr19:18653400-18655000	Active TSS	Gastric	stomach
36	chr19:18653400-18655000	Active TSS	Psoas Muscle	Psoas
37	chr19:18653400-18655000	Active TSS	K562	blood
38	chr19:18653600-18654600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr19:18653600-18654600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr19:18653600-18654600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr19:18653600-18654600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr19:18653600-18654600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
43	chr19:18653600-18654600	Active TSS	Primary B cells from peripheral blood	blood
44	chr19:18653600-18654600	Active TSS	Primary hematopoietic stem cells	blood
45	chr19:18653600-18654600	Active TSS	Primary hematopoietic stem cells short term culture	blood
46	chr19:18653600-18654600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
47	chr19:18653600-18654600	Active TSS	Primary T helper cells fromperipheralblood	blood
48	chr19:18653600-18654600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr19:18653600-18654600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr19:18653600-18654600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links