Variant report

Variant	rs10497520
Chromosome Location	chr2:179644855-179644856
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10178003	0.90[AMR][1000 genomes]
rs10497523	0.82[CHB][hapmap]
rs1484116	0.94[ASW][hapmap];0.82[GIH][hapmap];0.83[MKK][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes]
rs1484119	0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs2029395	0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2029397	0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2054708	0.87[MEX][hapmap]
rs2291313	0.94[ASW][hapmap];0.82[GIH][hapmap];0.89[LWK][hapmap];0.84[MKK][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes]
rs2562838	0.83[ASW][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes]
rs2742327	0.83[ASW][hapmap];0.84[YRI][hapmap]
rs3816849	0.82[CHB][hapmap]
rs4471922	0.82[GIH][hapmap]

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	nsv834470	chr2:179555152-179728726	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv934108	chr2:179556852-179729925	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10497520	TTN	cis	parietal	SCAN
rs10497520	SSFA2	cis	parietal	SCAN
rs10497520	PRKRA	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179533600-179669200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr2:179605400-179662400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:179610800-179671400	Weak transcription	Ovary	ovary
4	chr2:179614200-179645200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr2:179627000-179655200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr2:179627400-179653200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr2:179627600-179652600	Weak transcription	Brain Substantia Nigra	brain
8	chr2:179627600-179663800	Weak transcription	Thymus	Thymus
9	chr2:179629600-179666200	Weak transcription	GM12878-XiMat	blood
10	chr2:179630600-179651000	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr2:179631200-179649800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:179632000-179658800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr2:179632400-179667800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr2:179634200-179648600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr2:179634400-179645200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr2:179636200-179647000	Weak transcription	Lung	lung
17	chr2:179636200-179660600	Weak transcription	Brain Anterior Caudate	brain
18	chr2:179637200-179651000	Strong transcription	Primary T cells from cord blood	blood
19	chr2:179637200-179651000	Strong transcription	HSMMtube	muscle
20	chr2:179637600-179647000	Strong transcription	Fetal Muscle Leg	muscle
21	chr2:179639000-179672000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr2:179639400-179671400	Weak transcription	Gastric	stomach
23	chr2:179641200-179645400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr2:179641600-179647400	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr2:179641800-179646800	Weak transcription	Pancreas	Pancrea
26	chr2:179641800-179646800	Weak transcription	Right Ventricle	heart
27	chr2:179641800-179647000	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr2:179641800-179648800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr2:179642200-179650200	Weak transcription	Fetal Intestine Large	intestine
30	chr2:179642400-179647400	Weak transcription	Fetal Thymus	thymus
31	chr2:179642600-179645200	Weak transcription	Fetal Muscle Trunk	muscle
32	chr2:179642600-179646000	Genic enhancers	Fetal Heart	heart
33	chr2:179642600-179653000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
34	chr2:179642800-179647000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr2:179642800-179648800	Weak transcription	Primary hematopoietic stem cells	blood
36	chr2:179643600-179646800	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr2:179643800-179645200	Weak transcription	Primary B cells from cord blood	blood
38	chr2:179643800-179645600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
39	chr2:179643800-179647200	Weak transcription	HSMM	muscle
40	chr2:179644000-179645200	Weak transcription	Left Ventricle	heart
41	chr2:179644000-179645400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr2:179644400-179647400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:179644800-179646000	Strong transcription	Psoas Muscle	Psoas
44	chr2:179644800-179655400	Weak transcription	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links