Variant report

Variant	rs198560
Chromosome Location	chr13:48968713-48968714
allele	C/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	FOXA1	chr13:48968595-48968878	HepG2	liver:	n/a	n/a
2	FOXA1	chr13:48968606-48968976	HepG2	liver:	n/a	n/a
3	FOXA1	chr13:48968595-48968893	HepG2	liver:	n/a	n/a
4	FOXA2	chr13:48968645-48968802	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:48962225..48964484-chr13:48966549..48969073,2	K562	blood:

Variant related genes	Relation type
LPAR6	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs171991	0.84[AMR][1000 genomes]
rs174858	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs198566	0.96[AFR][1000 genomes]
rs198567	0.84[AFR][1000 genomes]
rs198572	0.84[AFR][1000 genomes]
rs198580	0.92[AFR][1000 genomes]
rs198589	0.91[AFR][1000 genomes]
rs198613	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs198626	0.86[EUR][1000 genomes]
rs2804087	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs2804088	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs2804089	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs2854363	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs2854364	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs411661	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs428431	0.98[AFR][1000 genomes]
rs443211	0.94[AFR][1000 genomes]
rs449151	0.89[AFR][1000 genomes]
rs4587857	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1803998	chr13:48966078-48986320	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48909000-48972200	Weak transcription	NHEK	skin
2	chr13:48914800-48972000	Weak transcription	NHLF	lung
3	chr13:48916800-48985400	Weak transcription	Colonic Mucosa	Colon
4	chr13:48920200-48974400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr13:48921600-48972000	Weak transcription	Stomach Mucosa	stomach
6	chr13:48925200-48974800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr13:48925400-48976400	Weak transcription	Ovary	ovary
8	chr13:48926800-48972000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr13:48928200-48971800	Weak transcription	A549	lung
10	chr13:48933400-48974000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr13:48934600-48984200	Weak transcription	Right Ventricle	heart
12	chr13:48936000-48974600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr13:48936400-48973200	Weak transcription	Hela-S3	cervix
14	chr13:48941800-48973200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr13:48943000-48970800	Weak transcription	Pancreas	Pancrea
16	chr13:48943600-48984200	Weak transcription	Brain Angular Gyrus	brain
17	chr13:48944000-48974400	Weak transcription	Brain Anterior Caudate	brain
18	chr13:48944200-48973800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr13:48944600-48983400	Weak transcription	Psoas Muscle	Psoas
20	chr13:48945000-48972000	Weak transcription	HSMMtube	muscle
21	chr13:48945400-48974400	Weak transcription	Small Intestine	intestine
22	chr13:48949400-48972800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr13:48953800-48972000	Weak transcription	Osteobl	bone
24	chr13:48954400-48972200	Weak transcription	HUVEC	blood vessel
25	chr13:48954800-48975000	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr13:48955800-48972000	Weak transcription	HMEC	breast
27	chr13:48955800-48972000	Weak transcription	NHDF-Ad	bronchial
28	chr13:48956000-48974000	Weak transcription	Colon Smooth Muscle	Colon
29	chr13:48956200-48970000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr13:48956200-48976600	Weak transcription	Liver	Liver
31	chr13:48959800-48972200	Weak transcription	Adipose Nuclei	Adipose
32	chr13:48961000-48969600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr13:48961000-48972000	Weak transcription	Fetal Lung	lung
34	chr13:48962400-48969200	Strong transcription	Dnd41	blood
35	chr13:48964000-48970000	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr13:48964000-48974400	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr13:48965000-48970400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr13:48965200-48974400	Weak transcription	Fetal Heart	heart
39	chr13:48965400-48969200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr13:48965600-48969000	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr13:48965600-48970000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr13:48966000-48969200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr13:48966000-48971800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr13:48966200-48970000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr13:48966200-48970200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr13:48966200-48971600	Weak transcription	Aorta	Aorta
47	chr13:48966400-48974200	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr13:48966400-48986000	Weak transcription	Lung	lung
49	chr13:48966800-48968800	Strong transcription	Primary T cells from cord blood	blood
50	chr13:48966800-48984200	Weak transcription	Placenta	Placenta

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