Variant report

Variant	rs315552
Chromosome Location	chr1:84795283-84795284
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1067072	0.93[ASN][1000 genomes]
rs1246546	0.90[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.96[ASN][1000 genomes]
rs1246549	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1246550	0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs160612	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1690702	1.00[CHB][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs1699157	0.93[ASN][1000 genomes]
rs170278	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17131613	0.92[GIH][hapmap]
rs172735	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17536473	1.00[CEU][hapmap]
rs178367	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];0.83[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs178368	0.92[ASN][1000 genomes]
rs186405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2055115	1.00[CEU][hapmap]
rs315520	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs315521	0.92[ASN][1000 genomes]
rs315522	0.92[ASN][1000 genomes]
rs315523	0.92[ASN][1000 genomes]
rs315524	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs315525	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs315526	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs315527	1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs315528	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs315530	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs315531	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs315532	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs315533	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs315535	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs315536	0.92[ASN][1000 genomes]
rs315538	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs315539	1.00[ASN][1000 genomes]
rs315540	0.97[ASN][1000 genomes]
rs315546	0.92[ASN][1000 genomes]
rs315547	0.99[ASN][1000 genomes]
rs315548	0.92[ASN][1000 genomes]
rs315549	0.92[ASN][1000 genomes]
rs315553	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs315554	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs315555	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs315556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316660	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs316661	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs316662	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs316663	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs316664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316665	0.93[ASN][1000 genomes]
rs511087	0.92[ASN][1000 genomes]
rs592464	0.93[ASN][1000 genomes]
rs786653	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[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	nsv830414	chr1:84636738-84824651	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv830426	chr1:84704924-84856229	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs315552	HIVEP2	trans	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84785800-84797800	Weak transcription	Gastric	stomach
2	chr1:84786600-84801600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr1:84787600-84796000	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr1:84789600-84795400	Weak transcription	Brain Angular Gyrus	brain
5	chr1:84789800-84797200	Weak transcription	Fetal Stomach	stomach
6	chr1:84790200-84795400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr1:84790600-84795800	Strong transcription	Rectal Mucosa Donor 31	rectum
8	chr1:84790800-84796400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr1:84791200-84795800	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr1:84792200-84795600	Weak transcription	Brain Substantia Nigra	brain
11	chr1:84792200-84797800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:84792400-84795400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr1:84792400-84795800	Weak transcription	Primary T cells from cord blood	blood
14	chr1:84792400-84797200	Weak transcription	Fetal Intestine Large	intestine
15	chr1:84793000-84798800	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr1:84793200-84796000	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr1:84793200-84796800	Weak transcription	Fetal Intestine Small	intestine
18	chr1:84793200-84797200	Weak transcription	Brain Hippocampus Middle	brain
19	chr1:84794600-84800800	Weak transcription	Primary hematopoietic stem cells	blood
20	chr1:84794800-84795800	Enhancers	Lung	lung
21	chr1:84794800-84801600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr1:84795000-84795600	Enhancers	H1 Cell Line	embryonic stem cell
23	chr1:84795000-84795600	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr1:84795000-84795800	Enhancers	H9 Cell Line	embryonic stem cell
25	chr1:84795000-84795800	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr1:84795000-84795800	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr1:84795000-84795800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr1:84795000-84795800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:84795000-84795800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:84795000-84796400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:84795000-84797400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:84795200-84795400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr1:84795200-84795400	Enhancers	Aorta	Aorta
34	chr1:84795200-84796200	Enhancers	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links