Variant report

Variant	rs17410853
Chromosome Location	chr3:47363971-47363972
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47363238..47365609-chr3:47422323..47423972,2	MCF-7	breast:
2	chr3:47357694..47362464-chr3:47362974..47365576,6	K562	blood:
3	chr3:47291130..47293100-chr3:47363237..47365913,2	K562	blood:
4	chr3:47363779..47366385-chr3:47368780..47371559,2	K562	blood:

Variant related genes	Relation type
ENSG00000260236	Chromatin interaction
ENSG00000076201	Chromatin interaction
ENSG00000239128	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1038394	0.88[CEU][hapmap]
rs10490798	0.95[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap]
rs1076394	0.85[CEU][hapmap];0.81[TSI][hapmap];0.86[YRI][hapmap]
rs10865946	0.88[CEU][hapmap]
rs11130123	0.82[CEU][hapmap]
rs11130124	0.85[CEU][hapmap]
rs11130126	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap]
rs11130127	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs11130128	0.88[CEU][hapmap]
rs11130129	0.88[CEU][hapmap]
rs11705957	0.88[CEU][hapmap];0.81[TSI][hapmap]
rs11710013	0.85[CEU][hapmap]
rs11710121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap]
rs11710322	0.85[CEU][hapmap];0.81[TSI][hapmap];0.86[YRI][hapmap]
rs11711265	0.88[CEU][hapmap]
rs11711824	0.88[CEU][hapmap]
rs11712445	0.91[CEU][hapmap]
rs11716763	0.88[CEU][hapmap]
rs11719877	0.88[CEU][hapmap]
rs11915074	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11920853	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11927371	0.83[AFR][1000 genomes]
rs12636851	0.88[CEU][hapmap]
rs13059519	0.88[CEU][hapmap]
rs13075233	0.88[CEU][hapmap]
rs13094438	0.85[CEU][hapmap]
rs1531875	0.88[CEU][hapmap]
rs1638676	0.85[CEU][hapmap]
rs17411375	0.86[ASW][hapmap];0.85[CEU][hapmap];0.81[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs17784882	0.85[ASW][hapmap];0.88[CEU][hapmap]
rs1872164	0.88[CEU][hapmap];0.81[TSI][hapmap]
rs2101247	0.85[CEU][hapmap]
rs2159400	0.80[ASW][hapmap];0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs2240796	0.95[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs2276853	0.85[CEU][hapmap]
rs2276854	0.85[CEU][hapmap]
rs2291298	0.87[CEU][hapmap]
rs295428	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs295441	0.85[CEU][hapmap]
rs295442	0.85[CEU][hapmap]
rs295449	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs295458	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs295461	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs3736177	0.87[CEU][hapmap]
rs3816779	0.88[CEU][hapmap]
rs4683326	0.87[CEU][hapmap]
rs4858811	0.88[CEU][hapmap]
rs4858824	0.88[CEU][hapmap]
rs4858868	0.88[CEU][hapmap]
rs4858888	0.83[AFR][1000 genomes]
rs4858890	0.88[AFR][1000 genomes]
rs4858893	0.88[CEU][hapmap]
rs4858894	0.82[CEU][hapmap]
rs553989	0.80[EUR][1000 genomes]
rs62246474	0.81[EUR][1000 genomes]
rs62248580	0.81[AMR][1000 genomes]
rs6768221	0.92[CEU][hapmap]
rs6772670	0.83[CEU][hapmap]
rs6780013	0.85[ASW][hapmap];0.96[CEU][hapmap];0.90[GIH][hapmap];0.87[LWK][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap]
rs6791842	0.85[CEU][hapmap]
rs6792461	0.88[CEU][hapmap]
rs6800271	0.88[CEU][hapmap]
rs7613282	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7651762	0.88[CEU][hapmap]
rs807931	0.82[EUR][1000 genomes]
rs807932	0.81[CEU][hapmap]
rs807936	0.85[CEU][hapmap]
rs811115	0.87[CEU][hapmap];0.81[CHB][hapmap]
rs8180040	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs878659	0.88[CEU][hapmap]
rs922957	0.88[CEU][hapmap]
rs9683033	0.88[CEU][hapmap]
rs9837343	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap]

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	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs17410853	C3orf75	cis	cerebellum	SCAN
rs17410853	HYAL2	cis	cerebellum	SCAN
rs17410853	LRRC2	cis	cerebellum	SCAN
rs17410853	SCAP	cis	parietal	SCAN
rs17410853	PRKAR2A	cis	cerebellum	SCAN
rs17410853	DHX30	cis	multi-tissue	Pritchard
rs17410853	IFRD2	cis	parietal	SCAN
rs17410853	CCR1	cis	cerebellum	SCAN
rs17410853	QRICH1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47325600-47367600	Weak transcription	A549	lung
2	chr3:47326400-47364400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:47328400-47364400	Weak transcription	Pancreas	Pancrea
4	chr3:47333200-47364800	Weak transcription	NH-A	brain
5	chr3:47333800-47371400	Weak transcription	Psoas Muscle	Psoas
6	chr3:47338600-47369800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr3:47338600-47371200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr3:47345000-47370000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr3:47345200-47365200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr3:47356400-47371200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr3:47356800-47382600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr3:47357000-47364800	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr3:47357000-47365000	Weak transcription	NHDF-Ad	bronchial
14	chr3:47357200-47364000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr3:47357200-47365200	Weak transcription	Small Intestine	intestine
16	chr3:47357200-47368800	Weak transcription	Primary hematopoietic stem cells	blood
17	chr3:47357200-47374800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr3:47358800-47387000	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr3:47359400-47365800	Strong transcription	Primary B cells from cord blood	blood
20	chr3:47359400-47385000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:47359400-47387200	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr3:47359400-47387800	Strong transcription	Spleen	Spleen
23	chr3:47359600-47364000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr3:47359600-47365000	Weak transcription	Colonic Mucosa	Colon
25	chr3:47359600-47386800	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr3:47359800-47364400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr3:47360000-47382600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr3:47360000-47388200	Strong transcription	Fetal Intestine Large	intestine
29	chr3:47360200-47365800	Strong transcription	Thymus	Thymus
30	chr3:47360400-47365000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:47360400-47365800	Strong transcription	GM12878-XiMat	blood
32	chr3:47360400-47387000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr3:47360400-47388000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr3:47360600-47364800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr3:47360600-47387000	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr3:47360600-47387200	Strong transcription	Primary B cells from peripheral blood	blood
37	chr3:47360600-47387600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr3:47360600-47387600	Strong transcription	Fetal Thymus	thymus
39	chr3:47360600-47387800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr3:47360600-47387800	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr3:47360600-47388200	Strong transcription	Duodenum Mucosa	Duodenum
42	chr3:47360600-47388800	Strong transcription	Primary T cells from cord blood	blood
43	chr3:47360800-47368600	Strong transcription	Fetal Intestine Small	intestine
44	chr3:47360800-47375200	Weak transcription	Fetal Heart	heart
45	chr3:47360800-47378800	Weak transcription	Fetal Kidney	kidney
46	chr3:47360800-47386800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr3:47360800-47388000	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr3:47361000-47364000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr3:47361000-47364800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr3:47361000-47365200	Strong transcription	HUES64 Cell Line	embryonic stem cell

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