Variant report

Variant	rs4775062
Chromosome Location	chr15:58801426-58801427
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:58800980..58802725-chr15:58817478..58819244,2	K562	blood:
2	chr15:58800669..58805424-chr15:58807712..58810883,4	K562	blood:
3	chr15:58787065..58789640-chr15:58800910..58803456,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11071384	0.94[EUR][1000 genomes]
rs12592017	0.94[CEU][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12898801	0.90[JPT][hapmap]
rs12898984	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12900448	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1869144	0.90[JPT][hapmap];0.85[MEX][hapmap]
rs1869145	0.88[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1968690	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1979177	0.94[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2414588	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2899631	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4581653	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4774301	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4774302	0.81[MEX][hapmap]
rs4775061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4775063	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4775064	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4775065	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.92[TSI][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4775066	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4775067	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57887591	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6494016	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66849766	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7180936	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7183248	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8038906	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv569598	chr15:58552606-58852463	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv3362898	chr15:58705732-58850860	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1043041	chr15:58744505-58876327	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv904268	chr15:58763678-58803225	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv569601	chr15:58800766-58866156	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4775062	CGNL1	cis	cerebellum	SCAN
rs4775062	ADAM10	cis	lymphoblastoid	seeQTL
rs4775062	KIAA1370	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58791400-58809400	Weak transcription	Spleen	Spleen
2	chr15:58793400-58803400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:58798600-58807800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr15:58798600-58813200	Weak transcription	Aorta	Aorta
5	chr15:58798800-58802200	Weak transcription	NHDF-Ad	bronchial
6	chr15:58798800-58802800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr15:58798800-58802800	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr15:58798800-58807800	Weak transcription	Primary B cells from cord blood	blood
9	chr15:58798800-58812600	Weak transcription	Left Ventricle	heart
10	chr15:58799000-58801800	Weak transcription	HSMM	muscle
11	chr15:58799000-58802400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr15:58799000-58804600	Weak transcription	Placenta	Placenta
13	chr15:58799000-58805000	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr15:58799000-58806000	Weak transcription	Psoas Muscle	Psoas
15	chr15:58799200-58802800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr15:58799200-58803400	Weak transcription	Esophagus	oesophagus
17	chr15:58799200-58807200	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr15:58799200-58809400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr15:58799400-58805000	Weak transcription	Fetal Thymus	thymus
20	chr15:58799400-58807800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr15:58799600-58802400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr15:58799600-58803400	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr15:58799800-58802600	Weak transcription	NHEK	skin
24	chr15:58799800-58802800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr15:58799800-58802800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr15:58800000-58802400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr15:58800000-58804600	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr15:58800400-58803200	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr15:58801000-58806600	Enhancers	HSMMtube	muscle
30	chr15:58801400-58801600	Enhancers	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links