Variant report

Variant	rs56141206
Chromosome Location	chr19:19115861-19115862
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	POLR2A	chr19:19115562-19115978	K562	blood:	n/a	n/a
2	POLR2A	chr19:19115672-19116033	HepG2	liver:	n/a	n/a
3	POLR2A	chr19:19115702-19116124	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:19106780..19109822-chr19:19115561..19117365,3	MCF-7	breast:
2	chr19:19111292..19114373-chr19:19114912..19119254,5	K562	blood:

Variant related genes	Relation type
SUGP2	TF binding region
ENSG00000064607	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10164302	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10221450	0.87[EUR][1000 genomes]
rs10221529	0.87[EUR][1000 genomes]
rs11549380	0.97[EUR][1000 genomes]
rs28498174	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4808171	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4808178	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4808180	0.97[EUR][1000 genomes]
rs4808181	0.87[EUR][1000 genomes]
rs4808896	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4808897	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4808899	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4808909	0.95[EUR][1000 genomes]
rs4808910	0.95[EUR][1000 genomes]
rs4808912	0.97[EUR][1000 genomes]
rs4808914	0.97[EUR][1000 genomes]
rs4808915	0.97[EUR][1000 genomes]
rs4808921	0.87[EUR][1000 genomes]
rs4808922	0.87[EUR][1000 genomes]
rs55658345	0.97[EUR][1000 genomes]
rs55678828	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56144126	0.87[EUR][1000 genomes]
rs56159042	0.84[EUR][1000 genomes]
rs56227420	0.87[EUR][1000 genomes]
rs60489867	0.97[EUR][1000 genomes]
rs60696741	0.97[EUR][1000 genomes]
rs72993458	0.87[EUR][1000 genomes]
rs72993462	0.85[EUR][1000 genomes]
rs73004898	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73004899	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73006907	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73006928	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73008923	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73008928	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73008930	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73008934	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73008939	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73008945	0.97[EUR][1000 genomes]
rs73008949	0.97[EUR][1000 genomes]
rs73008958	0.97[EUR][1000 genomes]
rs73008960	0.97[EUR][1000 genomes]
rs73010908	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	nsv2435	chr19:19077432-19122579	Strong transcription Bivalent Enhancer Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 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	chr19:19100200-19117400	Strong transcription	Fetal Intestine Small	intestine
2	chr19:19100600-19122800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr19:19101000-19125600	Strong transcription	Thymus	Thymus
4	chr19:19101000-19133000	Strong transcription	Fetal Thymus	thymus
5	chr19:19101200-19126000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr19:19101200-19130400	Strong transcription	Duodenum Mucosa	Duodenum
7	chr19:19101200-19140200	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr19:19101400-19130400	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr19:19101400-19142000	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr19:19101600-19130400	Strong transcription	Primary T cells from cord blood	blood
11	chr19:19101600-19130400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr19:19102000-19130200	Strong transcription	Sigmoid Colon	Sigmoid Colon
13	chr19:19102000-19132000	Strong transcription	Dnd41	blood
14	chr19:19102600-19122600	Weak transcription	Fetal Heart	heart
15	chr19:19103200-19130200	Strong transcription	Duodenum Smooth Muscle	Duodenum
16	chr19:19103600-19123600	Strong transcription	HepG2	liver
17	chr19:19106800-19119200	Weak transcription	Stomach Mucosa	stomach
18	chr19:19106800-19143000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr19:19107000-19119000	Weak transcription	Fetal Kidney	kidney
20	chr19:19107200-19130200	Strong transcription	Brain Germinal Matrix	brain
21	chr19:19107200-19142600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr19:19107400-19125800	Strong transcription	Fetal Muscle Leg	muscle
23	chr19:19107600-19127200	Strong transcription	Fetal Intestine Large	intestine
24	chr19:19107600-19130200	Strong transcription	Brain Hippocampus Middle	brain
25	chr19:19107600-19142600	Strong transcription	Fetal Stomach	stomach
26	chr19:19107800-19130200	Strong transcription	Placenta	Placenta
27	chr19:19107800-19130400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr19:19107800-19130400	Strong transcription	Fetal Brain Female	brain
29	chr19:19108000-19142000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr19:19108000-19142800	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr19:19108200-19116400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr19:19108200-19130400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr19:19108200-19142600	Weak transcription	Right Atrium	heart
34	chr19:19108600-19119600	Strong transcription	NHDF-Ad	bronchial
35	chr19:19108600-19130600	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr19:19108600-19142200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr19:19108600-19142800	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr19:19108800-19116200	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr19:19108800-19116200	Strong transcription	Rectal Smooth Muscle	rectum
40	chr19:19108800-19123800	Strong transcription	NHEK	skin
41	chr19:19108800-19127400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr19:19108800-19130400	Strong transcription	Primary B cells from peripheral blood	blood
43	chr19:19109000-19130400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr19:19109000-19141800	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr19:19109200-19121800	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr19:19109400-19130200	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr19:19109400-19130200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr19:19109400-19142400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr19:19109800-19130200	Strong transcription	GM12878-XiMat	blood
50	chr19:19110200-19130400	Strong transcription	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links