Variant report

Variant	rs2291313
Chromosome Location	chr2:179632710-179632711
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	FOS	chr2:179632650-179632758	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
TTN-AS1	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10497520	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]
rs1484116	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1484119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17076	0.86[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2562830	0.93[CEU][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs2562834	0.90[JPT][hapmap];0.84[TSI][hapmap]
rs2562836	0.86[CEU][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes]
rs2562838	0.88[ASW][hapmap];0.86[CEU][hapmap];0.90[JPT][hapmap];0.89[LWK][hapmap];0.87[MKK][hapmap];0.90[TSI][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2562839	0.86[CEU][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs2627043	0.93[CEU][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs2742327	0.88[ASW][hapmap];0.93[CEU][hapmap];0.90[JPT][hapmap];0.84[LWK][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2742331	0.86[CEU][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes]
rs4471922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.86[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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2291313	SSFA2	cis	parietal	SCAN
rs2291313	PRKRA	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179483200-179655400	Weak transcription	Adipose Nuclei	Adipose
2	chr2:179533600-179669200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr2:179577800-179640800	Weak transcription	Fetal Intestine Large	intestine
4	chr2:179590800-179640400	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr2:179605400-179662400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:179610800-179671400	Weak transcription	Ovary	ovary
7	chr2:179614200-179645200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr2:179619000-179636000	Strong transcription	Left Ventricle	heart
9	chr2:179620600-179634400	Weak transcription	Brain Anterior Caudate	brain
10	chr2:179622600-179640600	Weak transcription	Pancreas	Pancrea
11	chr2:179627000-179655200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr2:179627400-179636000	Weak transcription	Lung	lung
13	chr2:179627400-179653200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr2:179627600-179639200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr2:179627600-179652600	Weak transcription	Brain Substantia Nigra	brain
16	chr2:179627600-179663800	Weak transcription	Thymus	Thymus
17	chr2:179628000-179636400	Strong transcription	Primary T cells from cord blood	blood
18	chr2:179628000-179638600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
19	chr2:179629000-179636200	Genic enhancers	Fetal Heart	heart
20	chr2:179629600-179666200	Weak transcription	GM12878-XiMat	blood
21	chr2:179630600-179651000	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr2:179630800-179640800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr2:179631200-179633000	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr2:179631200-179634800	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr2:179631200-179649800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr2:179631400-179633000	Strong transcription	Skeletal Muscle Male	skeletal muscle
27	chr2:179631400-179636600	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr2:179631600-179635600	Strong transcription	Fetal Muscle Trunk	muscle
29	chr2:179631800-179632800	Enhancers	Brain Germinal Matrix	brain
30	chr2:179631800-179632800	Genic enhancers	HSMMtube	muscle
31	chr2:179632000-179632800	Enhancers	Muscle Satellite Cultured Cells	--
32	chr2:179632000-179632800	Genic enhancers	Fetal Muscle Leg	muscle
33	chr2:179632000-179632800	Strong transcription	Fetal Thymus	thymus
34	chr2:179632000-179633000	Enhancers	HSMM	muscle
35	chr2:179632000-179635600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr2:179632000-179658800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr2:179632200-179633200	Strong transcription	Primary B cells from cord blood	blood
38	chr2:179632400-179635000	Weak transcription	Psoas Muscle	Psoas
39	chr2:179632400-179635200	Strong transcription	Primary hematopoietic stem cells	blood
40	chr2:179632400-179636200	Strong transcription	Primary B cells from peripheral blood	blood
41	chr2:179632400-179667800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr2:179632600-179633400	Weak transcription	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links