Variant report

Variant	rs1052586
Chromosome Location	chr17:45018463-45018464
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:45003530..45006692-chr17:45016648..45018948,3	K562	blood:
2	chr17:45016816..45019749-chr17:45021342..45024491,3	K562	blood:
3	chr17:44999992..45001971-chr17:45015932..45018557,3	MCF-7	breast:
4	chr17:44953465..44954478-chr17:45017899..45018883,3	MCF-7	breast:
5	chr17:45016499..45018728-chr17:45019310..45022660,4	MCF-7	breast:
6	chr17:45000610..45002133-chr17:45017223..45020134,3	MCF-7	breast:
7	chr17:44928815..44931098-chr17:45016845..45019824,2	K562	blood:
8	chr17:44918866..44919832-chr17:45017923..45018908,3	K562	blood:
9	chr17:45017959..45019957-chr17:45020327..45022485,3	MCF-7	breast:
10	chr17:44998043..45003369-chr17:45017156..45021990,5	K562	blood:
11	chr17:37391660..37392353-chr17:45017960..45018854,3	MCF-7	breast:
12	chr17:45016346..45018666-chr17:45021157..45024902,5	K562	blood:
13	chr17:45012071..45014988-chr17:45016677..45019422,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000158955	Chromatin interaction
ENSG00000262633	Chromatin interaction
ENSG00000210709	Chromatin interaction
ENSG00000261886	Chromatin interaction
ENSG00000108433	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1047779	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1052504	0.99[ASN][1000 genomes]
rs10853085	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10853087	0.99[ASN][1000 genomes]
rs11079742	0.88[CEU][hapmap];0.81[JPT][hapmap];0.88[EUR][1000 genomes]
rs11079745	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11079750	0.81[CEU][hapmap]
rs11652318	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11654971	0.99[ASN][1000 genomes]
rs11655668	0.85[JPT][hapmap]
rs11656362	0.98[ASN][1000 genomes]
rs11658276	0.98[ASN][1000 genomes]
rs11869840	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12601886	0.99[ASN][1000 genomes]
rs12940071	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1618989	0.99[ASN][1000 genomes]
rs1623402	0.99[ASN][1000 genomes]
rs1662576	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1662577	0.99[ASN][1000 genomes]
rs1662594	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1662596	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1662597	0.97[ASN][1000 genomes]
rs17608961	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1838105	0.81[JPT][hapmap]
rs1867237	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs189899	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs197912	0.95[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs197913	0.88[ASN][1000 genomes]
rs197915	0.91[ASN][1000 genomes]
rs197917	0.98[ASN][1000 genomes]
rs197918	0.99[ASN][1000 genomes]
rs197919	0.99[ASN][1000 genomes]
rs197922	0.81[JPT][hapmap]
rs197923	0.81[JPT][hapmap]
rs197925	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs197926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2003538	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2003539	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2072317	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs2191033	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2316330	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2317997	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28553405	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2920396	0.99[ASN][1000 genomes]
rs2920397	0.99[ASN][1000 genomes]
rs35707546	0.97[ASN][1000 genomes]
rs3760377	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3785888	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3785889	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs3809854	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3851784	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3851785	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3851786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3851787	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4074249	0.80[CEU][hapmap]
rs4381655	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4602097	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4968248	0.96[ASN][1000 genomes]
rs4968250	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4968285	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4968286	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4968287	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4968288	0.99[ASN][1000 genomes]
rs4968290	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4968304	0.80[CEU][hapmap]
rs61671555	0.85[EUR][1000 genomes]
rs62075889	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62075896	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6504622	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7213526	0.98[ASN][1000 genomes]
rs7216991	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7225428	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7342957	0.99[ASN][1000 genomes]
rs736603	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs736604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs740617	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs758391	0.88[CEU][hapmap];0.81[JPT][hapmap];0.87[EUR][1000 genomes]
rs758392	0.88[CEU][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs9303532	0.85[EUR][1000 genomes]
rs9889741	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9889762	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9893713	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9898527	0.85[EUR][1000 genomes]
rs9898981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9901977	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9910899	0.85[EUR][1000 genomes]
rs9911366	0.85[EUR][1000 genomes]
rs9911967	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9912794	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3492820	chr17:44174959-45161556	Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv3492821	chr17:44174959-45161556	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	esv3502492	chr17:44305975-45169159	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	esv3502493	chr17:44305975-45169159	Active TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv531823	chr17:44485771-45067769	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv908562	chr17:44828931-45102413	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv949295	chr17:44836653-45080757	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
8	nsv428672	chr17:44872446-45023425	Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1067211	chr17:44979111-45057620	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
10	nsv543378	chr17:44979111-45057620	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1052586	GOSR2	cis	multi-tissue	Pritchard
rs1052586	GOSR2	cis	normal skin	skin_eQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45001600-45020800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr17:45002000-45021000	Weak transcription	Fetal Heart	heart
3	chr17:45002800-45020000	Strong transcription	Fetal Muscle Leg	muscle
4	chr17:45005000-45019800	Strong transcription	GM12878-XiMat	blood
5	chr17:45005200-45018800	Strong transcription	Primary B cells from peripheral blood	blood
6	chr17:45005400-45018800	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr17:45005600-45018600	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr17:45005600-45020200	Strong transcription	Fetal Thymus	thymus
9	chr17:45005800-45019800	Strong transcription	Fetal Muscle Trunk	muscle
10	chr17:45005800-45020000	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr17:45006200-45020000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr17:45006400-45018600	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr17:45006600-45019000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr17:45006600-45019800	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr17:45006800-45018600	Strong transcription	Muscle Satellite Cultured Cells	--
16	chr17:45006800-45018800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr17:45006800-45018800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr17:45006800-45019400	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr17:45006800-45019800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr17:45006800-45020000	Strong transcription	Dnd41	blood
21	chr17:45007000-45018600	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr17:45007000-45018600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr17:45007000-45018800	Strong transcription	Osteobl	bone
24	chr17:45007000-45019000	Strong transcription	Brain Germinal Matrix	brain
25	chr17:45007000-45019800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr17:45007000-45019800	Strong transcription	HSMM	muscle
27	chr17:45007200-45018600	Strong transcription	Stomach Smooth Muscle	stomach
28	chr17:45007200-45018600	Strong transcription	NHLF	lung
29	chr17:45007200-45018800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr17:45007200-45019600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr17:45007400-45018600	Strong transcription	Colon Smooth Muscle	Colon
32	chr17:45007600-45020000	Strong transcription	A549	lung
33	chr17:45007800-45018800	Strong transcription	HMEC	breast
34	chr17:45007800-45018800	Strong transcription	NH-A	brain
35	chr17:45007800-45019800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr17:45008200-45018800	Strong transcription	HSMMtube	muscle
37	chr17:45008800-45019600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr17:45009200-45019800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr17:45009400-45018800	Strong transcription	HUVEC	blood vessel
40	chr17:45009800-45019800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr17:45012800-45040000	Weak transcription	Hela-S3	cervix
42	chr17:45013400-45020200	Weak transcription	Fetal Brain Male	brain
43	chr17:45013600-45019000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr17:45013600-45019800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr17:45013800-45019600	Strong transcription	Duodenum Mucosa	Duodenum
46	chr17:45014000-45018600	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr17:45014000-45018800	Strong transcription	Fetal Intestine Large	intestine
48	chr17:45014000-45020000	Strong transcription	Lung	lung
49	chr17:45014000-45020200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr17:45014000-45020200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links