Variant report

Variant	rs2716734
Chromosome Location	chr2:39947721-39947722
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	chr2:39947562..39949942-chr2:39951658..39954303,2	MCF-7	breast:
2	chr2:39946231..39948617-chr2:39954711..39957133,2	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 49 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10198734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13388310	1.00[CHB][hapmap]
rs13395966	1.00[EUR][1000 genomes]
rs13430261	1.00[MEX][hapmap]
rs17024154	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17024276	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17024299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17024307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17024325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2058621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2110672	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs2110673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs2160207	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs2192712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2540234	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2716706	1.00[EUR][1000 genomes]
rs2716724	0.96[EUR][1000 genomes]
rs2716726	0.96[EUR][1000 genomes]
rs57704430	1.00[EUR][1000 genomes]
rs60003713	1.00[EUR][1000 genomes]
rs6708232	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6716262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6742533	1.00[MEX][hapmap]
rs6745129	1.00[EUR][1000 genomes]
rs73924917	1.00[EUR][1000 genomes]
rs73924918	1.00[EUR][1000 genomes]
rs73924919	1.00[EUR][1000 genomes]
rs73924920	1.00[EUR][1000 genomes]
rs73924934	1.00[EUR][1000 genomes]
rs7576551	0.88[EUR][1000 genomes]
rs7604790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873889	chr2:39830183-39950482	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv833870	chr2:39837022-40026024	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS 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
3	nsv833881	chr2:39914558-40067256	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Erectile dysfunction and prostate cancer treatment	20932654	GWAS catalog

mRNA abundance (count:48)

SNP	Gene	Cis/trans	Tissue	Source
rs2716734	SERINC5	trans	brain	seeQTL
rs2716734	C4orf34	trans	brain	seeQTL
rs2716734	NUDT12	trans	brain	seeQTL
rs2716734	ADAL	trans	brain	seeQTL
rs2716734	SPC24	trans	brain	seeQTL
rs2716734	TMEM156	trans	brain	seeQTL
rs2716734	ZNF620	trans	brain	seeQTL
rs2716734	HLA-G	trans	brain	seeQTL
rs2716734	TREML1	trans	brain	seeQTL
rs2716734	RNF11	trans	brain	seeQTL
rs2716734	NDUFC2	trans	brain	seeQTL
rs2716734	EVI5	trans	brain	seeQTL
rs2716734	SRD5A3	trans	brain	seeQTL
rs2716734	LLPH	trans	brain	seeQTL
rs2716734	MLLT1	trans	brain	seeQTL
rs2716734	CBWD1	trans	brain	seeQTL
rs2716734	NACA2	trans	brain	seeQTL
rs2716734	CCDC82	trans	brain	seeQTL
rs2716734	METTL2B	trans	brain	seeQTL
rs2716734	MED23	trans	brain	seeQTL
rs2716734	PLTP	trans	brain	seeQTL
rs2716734	RBM39	trans	brain	seeQTL
rs2716734	USH1G	trans	brain	seeQTL
rs2716734	APOBEC3C	trans	brain	seeQTL
rs2716734	CSAD	trans	brain	seeQTL
rs2716734	IDO2	trans	brain	seeQTL
rs2716734	OLIG3	trans	brain	seeQTL
rs2716734	ZNF667	trans	brain	seeQTL
rs2716734	SIPA1L3	trans	brain	seeQTL
rs2716734	KRTAP10-10	trans	brain	seeQTL
rs2716734	HIST1H4D	trans	brain	seeQTL
rs2716734	ITFG1	trans	brain	seeQTL
rs2716734	GOLGA6L9	trans	brain	seeQTL
rs2716734	CXCL11	trans	brain	seeQTL
rs2716734	PIGX	trans	brain	seeQTL
rs2716734	ZNF568	trans	brain	seeQTL
rs2716734	TCF7	trans	brain	seeQTL
rs2716734	CTU1	trans	brain	seeQTL
rs2716734	ELMOD3	trans	brain	seeQTL
rs2716734	NIPSNAP3A	trans	brain	seeQTL
rs2716734	ABI1	trans	brain	seeQTL
rs2716734	C14orf126	trans	brain	seeQTL
rs2716734	PPIG	trans	brain	seeQTL
rs2716734	ANP32A	trans	brain	seeQTL
rs2716734	UQCRB	trans	brain	seeQTL
rs2716734	C2orf69	trans	brain	seeQTL
rs2716734	STXBP4	trans	brain	seeQTL
rs2716734	CROT	trans	brain	seeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39925000-39957600	Weak transcription	Fetal Stomach	stomach
2	chr2:39925200-39950000	Weak transcription	Left Ventricle	heart
3	chr2:39931400-39957600	Weak transcription	Fetal Muscle Leg	muscle
4	chr2:39936600-39950600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:39937400-39948400	Weak transcription	Fetal Heart	heart
6	chr2:39938000-39957600	Weak transcription	Fetal Brain Female	brain
7	chr2:39938200-39950600	Weak transcription	HSMMtube	muscle
8	chr2:39938400-39950000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:39938800-39947800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:39940800-39950800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:39942000-39963000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr2:39943200-39956200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr2:39944400-39976600	Weak transcription	Fetal Brain Male	brain
14	chr2:39945200-39954400	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr2:39946400-39948000	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr2:39946400-39950600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr2:39946600-39949800	Weak transcription	Psoas Muscle	Psoas
18	chr2:39946600-39951200	Weak transcription	Aorta	Aorta
19	chr2:39946800-39950000	Weak transcription	NH-A	brain
20	chr2:39946800-39950600	Weak transcription	Osteobl	bone
21	chr2:39946800-39959600	Weak transcription	Brain Germinal Matrix	brain
22	chr2:39947000-39948600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:39947200-39948200	Weak transcription	Brain Anterior Caudate	brain
24	chr2:39947600-39947800	Enhancers	Brain Cingulate Gyrus	brain
25	chr2:39947600-39947800	Bivalent Enhancer	Brain Hippocampus Middle	brain
26	chr2:39947600-39947800	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr2:39947600-39948200	Enhancers	H1 Cell Line	embryonic stem cell
28	chr2:39947600-39948400	Enhancers	H9 Cell Line	embryonic stem cell
29	chr2:39947600-39948800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr2:39947600-39949000	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr2:39947600-39949000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links