Variant report

Variant	rs55658345
Chromosome Location	chr19:19173556-19173557
allele	A/C
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	PML	chr19:19173241-19174472	K562	blood:	n/a	n/a
2	IRF1	chr19:19173079-19173651	K562	blood:	n/a	chr19:19173210-19173217
3	FOS	chr19:19173289-19173647	MCF10A-Er-Src	breast:	n/a	chr19:19173411-19173418 chr19:19173406-19173417 chr19:19173409-19173418 chr19:19173408-19173420 chr19:19173408-19173419
4	MXI1	chr19:19173437-19173577	K562	blood:	n/a	n/a
5	RCOR1	chr19:19172800-19175463	IMR90	lung:	n/a	n/a
6	HDAC2	chr19:19173186-19173808	K562	blood:	n/a	n/a
7	MYC	chr19:19173277-19175247	K562	blood:	n/a	n/a
8	CBX3	chr19:19173110-19174697	K562	blood:	n/a	n/a
9	ARID3A	chr19:19173214-19174819	K562	blood:	n/a	n/a
10	POLR2A	chr19:19173384-19173557	H1-hESC	embryonic stem cell:	n/a	n/a
11	JUN	chr19:19172291-19175360	K562	blood:	n/a	chr19:19173411-19173418 chr19:19173406-19173417 chr19:19173409-19173418 chr19:19173408-19173420 chr19:19174664-19174673
12	RCOR1	chr19:19172826-19175177	K562	blood:	n/a	n/a
13	USF1	chr19:19173368-19173732	K562	blood:	n/a	n/a
14	POLR2A	chr19:19172863-19174890	H1-hESC	embryonic stem cell:	n/a	n/a
15	ATF3	chr19:19173191-19173662	K562	blood:	n/a	n/a
16	POLR2A	chr19:19172969-19175517	HepG2	liver:	n/a	n/a
17	POLR2A	chr19:19173137-19174884	K562	blood:	n/a	n/a
18	POLR2A	chr19:19171636-19174879	PFSK-1	brain:	n/a	n/a
19	BHLHE40	chr19:19173291-19175133	K562	blood:	n/a	n/a
20	MYC	chr19:19173365-19173565	NB4	blood:	n/a	n/a
21	NFATC1	chr19:19173354-19174957	GM12878	blood:	n/a	n/a
22	CUX1	chr19:19173238-19173571	K562	blood:	n/a	n/a
23	FOS	chr19:19173259-19173600	MCF10A-Er-Src	breast:	n/a	chr19:19173411-19173418 chr19:19173406-19173417 chr19:19173409-19173418 chr19:19173408-19173420 chr19:19173408-19173419
24	HCFC1	chr19:19173482-19173584	K562	blood:	n/a	n/a
25	MAZ	chr19:19173269-19175483	K562	blood:	n/a	n/a
26	TFAP2C	chr19:19173071-19175223	Hela-S3	cervix:	n/a	chr19:19174363-19174378
27	JUN	chr19:19173233-19173626	K562	blood:	n/a	chr19:19173411-19173418 chr19:19173406-19173417 chr19:19173409-19173418 chr19:19173408-19173420
28	UBTF	chr19:19173227-19173621	K562	blood:	n/a	n/a
29	MAX	chr19:19173314-19173632	K562	blood:	n/a	n/a
30	JUND	chr19:19173150-19173836	SK-N-SH	brain:	n/a	chr19:19173411-19173418 chr19:19173406-19173417 chr19:19173409-19173418 chr19:19173408-19173419 chr19:19173408-19173420
31	MTA3	chr19:19173407-19175939	GM12878	blood:	n/a	n/a
32	POLR2A	chr19:19173152-19173603	SK-N-SH	brain:	n/a	n/a
33	HDAC2	chr19:19173255-19173560	K562	blood:	n/a	n/a
34	FOSL1	chr19:19173093-19173673	K562	blood:	n/a	chr19:19173411-19173418 chr19:19173406-19173417 chr19:19173409-19173418 chr19:19173408-19173419 chr19:19173408-19173420
35	JUN	chr19:19173255-19173659	K562	blood:	n/a	chr19:19173411-19173418 chr19:19173406-19173417 chr19:19173409-19173418 chr19:19173408-19173420
36	MAFF	chr19:19173143-19173651	K562	blood:	n/a	n/a
37	POLR2A	chr19:19173105-19175157	K562	blood:	n/a	n/a
38	RCOR1	chr19:19173342-19175147	HepG2	liver:	n/a	n/a
39	FOS	chr19:19173259-19173603	MCF10A-Er-Src	breast:	n/a	chr19:19173411-19173418 chr19:19173406-19173417 chr19:19173409-19173418 chr19:19173408-19173420 chr19:19173408-19173419
40	NR2F2	chr19:19173079-19174771	K562	blood:	n/a	n/a
41	MAX	chr19:19173201-19176107	K562	blood:	n/a	chr19:19176021-19176031 chr19:19175555-19175566 chr19:19175557-19175564
42	POLR2A	chr19:19173196-19173644	K562	blood:	n/a	n/a
43	POLR2A	chr19:19172219-19174905	PANC-1	pancreas:	n/a	n/a
44	TEAD4	chr19:19173129-19174474	K562	blood:	n/a	n/a
45	ZNF143	chr19:19173275-19175142	K562	blood:	n/a	chr19:19173292-19173311
46	ATF3	chr19:19173341-19173568	K562	blood:	n/a	n/a
47	ZMIZ1	chr19:19173103-19174782	K562	blood:	n/a	n/a
48	MYC	chr19:19173292-19175233	K562	blood:	n/a	n/a
49	FOSL2	chr19:19173227-19173629	SK-N-SH	brain:	n/a	chr19:19173411-19173418 chr19:19173406-19173417 chr19:19173409-19173418 chr19:19173408-19173420
50	POLR2A	chr19:19173295-19174948	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:19172859..19177096-chr19:19213191..19220004,7	K562	blood:
2	chr19:19169646..19176603-chr19:19241603..19250623,23	K562	blood:
3	chr19:19141992..19145925-chr19:19172787..19177854,10	K562	blood:
4	chr19:19129913..19132824-chr19:19171752..19174736,2	K562	blood:
5	chr19:19170341..19177029-chr19:19229928..19235464,11	K562	blood:
6	chr19:19170465..19178046-chr19:19213939..19220242,15	K562	blood:
7	chr19:19171269..19173626-chr19:19203292..19205531,2	K562	blood:
8	chr19:19171826..19174275-chr19:19223519..19227124,3	K562	blood:
9	chr19:19172595..19175925-chr19:19247411..19251399,4	MCF-7	breast:
10	chr19:19169419..19177029-chr19:19229685..19233171,13	K562	blood:
11	chr19:19161417..19167211-chr19:19171135..19175299,5	MCF-7	breast:
12	chr19:19141992..19145825-chr19:19171077..19177701,15	K562	blood:
13	chr19:19169646..19176667-chr19:19241603..19249514,19	K562	blood:

Variant related genes	Relation type
SLC25A42	TF binding region
ENSG00000064545	Chromatin interaction
ENSG00000181035	Chromatin interaction
ENSG00000105676	Chromatin interaction
ENSG00000064607	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10164302	0.95[EUR][1000 genomes]
rs10221450	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10221529	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11549380	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28498174	0.97[EUR][1000 genomes]
rs4808171	0.97[EUR][1000 genomes]
rs4808178	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4808180	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4808181	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4808896	0.97[EUR][1000 genomes]
rs4808897	0.97[EUR][1000 genomes]
rs4808899	0.97[EUR][1000 genomes]
rs4808909	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4808910	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4808912	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4808914	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4808915	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4808921	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4808922	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55678828	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs56141206	0.97[EUR][1000 genomes]
rs56144126	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56159042	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56227420	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60489867	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60696741	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72993458	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72993462	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73004898	0.97[EUR][1000 genomes]
rs73004899	0.97[EUR][1000 genomes]
rs73006907	0.97[EUR][1000 genomes]
rs73006925	1.00[AFR][1000 genomes]
rs73006928	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73008923	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73008928	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73008930	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73008934	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73008939	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73008945	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73008949	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73008958	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73008960	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73010908	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833778	chr19:19012669-19201487	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
2	nsv1059305	chr19:19131310-19209999	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
3	nsv543927	chr19:19147376-19178024	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
4	nsv833779	chr19:19163492-19313091	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19145000-19174000	Weak transcription	Small Intestine	intestine
2	chr19:19145600-19173800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr19:19145600-19173800	Weak transcription	Fetal Kidney	kidney
4	chr19:19151000-19173800	Weak transcription	Fetal Brain Male	brain
5	chr19:19151800-19173800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr19:19151800-19173800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr19:19153200-19173600	Strong transcription	Fetal Stomach	stomach
8	chr19:19160400-19173600	Strong transcription	Fetal Brain Female	brain
9	chr19:19162800-19173800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr19:19166000-19173800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr19:19166200-19173800	Weak transcription	Colon Smooth Muscle	Colon
12	chr19:19166400-19173800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr19:19166400-19174000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr19:19167000-19173800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr19:19167400-19173800	Genic enhancers	Fetal Muscle Trunk	muscle
16	chr19:19167400-19173800	Genic enhancers	Fetal Muscle Leg	muscle
17	chr19:19168600-19173800	Weak transcription	Primary B cells from cord blood	blood
18	chr19:19168600-19173800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr19:19168800-19173800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr19:19168800-19174000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr19:19169000-19173600	Weak transcription	Primary B cells from peripheral blood	blood
22	chr19:19169000-19173600	Strong transcription	Fetal Intestine Small	intestine
23	chr19:19169000-19174000	Weak transcription	Ovary	ovary
24	chr19:19169400-19173600	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr19:19169400-19173600	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr19:19169400-19173800	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr19:19169400-19173800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr19:19169600-19173800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr19:19169600-19174000	Weak transcription	Aorta	Aorta
30	chr19:19169800-19173800	Enhancers	HepG2	liver
31	chr19:19170000-19173600	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr19:19170000-19173800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr19:19170400-19173800	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr19:19170600-19173600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr19:19170600-19173600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr19:19170600-19173800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr19:19170600-19173800	Enhancers	Liver	Liver
38	chr19:19170600-19173800	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr19:19170600-19173800	Weak transcription	GM12878-XiMat	blood
40	chr19:19170600-19174200	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr19:19170800-19173600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr19:19170800-19173600	Weak transcription	Brain Angular Gyrus	brain
43	chr19:19170800-19173600	Weak transcription	Placenta	Placenta
44	chr19:19170800-19173600	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr19:19170800-19173600	Weak transcription	Stomach Smooth Muscle	stomach
46	chr19:19170800-19173800	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr19:19170800-19173800	Weak transcription	Primary T cells from cord blood	blood
48	chr19:19170800-19173800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr19:19170800-19173800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr19:19170800-19174000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links