Variant report

Variant	rs2952275
Chromosome Location	chr17:66518663-66518664
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	chr17:66509486..66513635-chr17:66517582..66519968,5	K562	blood:
2	chr17:66517930..66519994-chr17:66524115..66526694,2	K562	blood:

Variant related genes	Relation type
ENSG00000108946	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10468445	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286558	0.82[CHB][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2302230	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2302231	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28521534	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2907373	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2907374	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2952271	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4265886	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4561532	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7217296	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7219227	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7222188	0.80[CEU][hapmap]
rs8066131	0.80[CEU][hapmap];0.84[MEX][hapmap]
rs8076465	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	nsv932935	chr17:66511434-66518806	Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv933839	chr17:66511434-66518903	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2952275	ABCA8	cis	cerebellum	SCAN
rs2952275	CD79B	cis	cerebellum	SCAN
rs2952275	WIPI1	cis	parietal	SCAN
rs2952275	PRKAR1A	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66509600-66525800	Weak transcription	Pancreas	Pancrea
2	chr17:66511600-66537000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr17:66511600-66537000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr17:66511800-66518800	Weak transcription	Small Intestine	intestine
5	chr17:66511800-66522200	Weak transcription	Fetal Brain Male	brain
6	chr17:66511800-66531600	Strong transcription	Fetal Intestine Large	intestine
7	chr17:66511800-66536600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr17:66511800-66537000	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr17:66511800-66537800	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr17:66512000-66530000	Strong transcription	HSMM	muscle
11	chr17:66513200-66528600	Strong transcription	Muscle Satellite Cultured Cells	--
12	chr17:66513200-66533000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr17:66513400-66519200	Strong transcription	Fetal Stomach	stomach
14	chr17:66514200-66519200	Weak transcription	Fetal Lung	lung
15	chr17:66514200-66528800	Strong transcription	HepG2	liver
16	chr17:66514400-66520600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr17:66514600-66524000	Weak transcription	Aorta	Aorta
18	chr17:66514600-66524000	Weak transcription	Esophagus	oesophagus
19	chr17:66514600-66526400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr17:66514800-66518800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr17:66514800-66518800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr17:66514800-66518800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr17:66514800-66518800	Weak transcription	Brain Germinal Matrix	brain
24	chr17:66514800-66518800	Weak transcription	Colonic Mucosa	Colon
25	chr17:66514800-66518800	Weak transcription	Lung	lung
26	chr17:66514800-66519000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr17:66514800-66519200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr17:66514800-66520000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr17:66514800-66522800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr17:66514800-66523000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr17:66514800-66523200	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr17:66514800-66525600	Weak transcription	Spleen	Spleen
33	chr17:66514800-66527800	Strong transcription	Fetal Muscle Trunk	muscle
34	chr17:66514800-66537000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr17:66514800-66537400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr17:66514800-66537600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr17:66515000-66518800	Weak transcription	Brain Angular Gyrus	brain
38	chr17:66515000-66523000	Weak transcription	Stomach Mucosa	stomach
39	chr17:66515000-66535800	Strong transcription	Placenta	Placenta
40	chr17:66515200-66519200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr17:66515200-66533400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr17:66515200-66534600	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr17:66515400-66521800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr17:66515400-66521800	Weak transcription	Right Ventricle	heart
45	chr17:66515600-66518800	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr17:66515600-66518800	Weak transcription	Psoas Muscle	Psoas
47	chr17:66515800-66520000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr17:66516200-66518800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr17:66516200-66519000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr17:66516200-66519000	Weak transcription	Hela-S3	cervix

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