Variant report

Variant	rs17252200
Chromosome Location	chr13:51961400-51961401
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:51959134..51961591-chr13:52026035..52028339,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SERPINE3-1	chr13:51961129-51961479	NONHSAT033902
2	lnc-SERPINE3-1	chr13:51961129-51961479	NONHSAT033903

Variant related genes	Relation type
ENSG00000236778	Chromatin interaction
ENSG00000102786	Chromatin interaction
ENSG00000224892	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11148219	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs1547710	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17252166	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17252173	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17252180	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17252193	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17837214	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17837215	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17837216	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17837217	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4941699	0.89[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs4942995	0.89[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs4942996	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs4942999	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs57845363	0.81[ASN][1000 genomes]
rs61749884	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61749885	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7330735	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs74087486	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7984158	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7992891	0.89[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs7995478	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7995885	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8000429	1.00[CHB][hapmap];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8000433	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8001333	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8002112	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9316537	0.83[CHD][hapmap]
rs9563049	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs9563055	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs9563058	1.00[MEX][hapmap]
rs9563062	1.00[MEX][hapmap]
rs9568580	0.89[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap]
rs9568586	0.89[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap]
rs9568631	0.86[CHB][hapmap]
rs9591402	0.82[CHD][hapmap];0.82[JPT][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17252200	Hs.123474	cis	multi-tissue	Pritchard

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51934400-51963800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr13:51935600-51971400	Weak transcription	Gastric	stomach
3	chr13:51935800-51962000	Strong transcription	Dnd41	blood
4	chr13:51936200-51963600	Strong transcription	Liver	Liver
5	chr13:51936400-51966000	Weak transcription	Right Ventricle	heart
6	chr13:51937400-51961800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr13:51938600-51961800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr13:51939200-51970600	Weak transcription	Brain Angular Gyrus	brain
9	chr13:51939400-51962200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr13:51944800-51964200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr13:51945000-51964400	Strong transcription	HSMM	muscle
12	chr13:51945200-51970600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr13:51945200-51971600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr13:51945400-51970600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr13:51945600-51961600	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr13:51945800-51961400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr13:51945800-52016600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr13:51946200-51963200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr13:51946200-51988000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr13:51946400-51971600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr13:51946600-51963600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr13:51947000-51963600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr13:51947000-51970800	Weak transcription	Brain Hippocampus Middle	brain
24	chr13:51948000-51970800	Weak transcription	A549	lung
25	chr13:51948000-51971400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr13:51948600-51962800	Weak transcription	Brain Anterior Caudate	brain
27	chr13:51948600-51971600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr13:51948600-51971600	Weak transcription	Small Intestine	intestine
29	chr13:51949000-51966400	Weak transcription	Psoas Muscle	Psoas
30	chr13:51949000-51971400	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr13:51949400-51971400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr13:51949400-51971400	Weak transcription	Esophagus	oesophagus
33	chr13:51949400-51971400	Weak transcription	Pancreas	Pancrea
34	chr13:51949400-52025000	Weak transcription	Fetal Muscle Leg	muscle
35	chr13:51950000-51970600	Weak transcription	Brain Substantia Nigra	brain
36	chr13:51950000-51971400	Weak transcription	Fetal Stomach	stomach
37	chr13:51950000-51971400	Weak transcription	Left Ventricle	heart
38	chr13:51950000-51971800	Weak transcription	Lung	lung
39	chr13:51950000-52025200	Weak transcription	Fetal Muscle Trunk	muscle
40	chr13:51950200-51999800	Weak transcription	Brain Germinal Matrix	brain
41	chr13:51951800-51970600	Weak transcription	Hela-S3	cervix
42	chr13:51952400-51970600	Weak transcription	Stomach Smooth Muscle	stomach
43	chr13:51952400-51971400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr13:51952600-51963000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr13:51952600-51970800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr13:51952600-51970800	Weak transcription	HSMMtube	muscle
47	chr13:51952600-51971400	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr13:51953200-51970600	Weak transcription	Colon Smooth Muscle	Colon
49	chr13:51954000-51970600	Weak transcription	K562	blood
50	chr13:51954600-51963200	Weak transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links