Variant report

Variant	rs17689625
Chromosome Location	chr16:79748962-79748963
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	chr16:79748215..79750432-chr16:79755525..79757544,2	MCF-7	breast:
2	chr16:79744125..79746553-chr16:79748554..79750825,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MAF-2	chr16:79748640-79750737	XLOC_012017

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs11150187	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs11150188	0.89[EUR][1000 genomes]
rs11150189	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11150190	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11150191	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11642757	0.84[EUR][1000 genomes]
rs11644082	0.82[EUR][1000 genomes]
rs11644758	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs11644799	0.84[EUR][1000 genomes]
rs11644836	0.88[EUR][1000 genomes]
rs11645076	0.84[EUR][1000 genomes]
rs11646791	0.89[EUR][1000 genomes]
rs11864901	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11865979	0.86[EUR][1000 genomes]
rs12149203	0.86[EUR][1000 genomes]
rs12444166	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs12449109	0.84[EUR][1000 genomes]
rs12449161	0.86[EUR][1000 genomes]
rs1345901	0.80[EUR][1000 genomes]
rs1424231	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs16950982	0.89[EUR][1000 genomes]
rs16950997	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs17689024	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17689159	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17689455	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17767383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17767419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17767491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17767742	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17767904	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28773265	0.81[EUR][1000 genomes]
rs3813580	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813582	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4334315	0.86[AFR][1000 genomes]
rs4575545	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56738967	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56892402	0.84[EUR][1000 genomes]
rs57652769	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58722186	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59617251	0.81[EUR][1000 genomes]
rs7187128	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs7188445	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7190187	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7195321	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7202240	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7202770	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs7203756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73575076	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73575079	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73575083	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73575085	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73575086	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73575095	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74037508	0.84[EUR][1000 genomes]
rs74037509	0.83[EUR][1000 genomes]
rs8047723	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs8048928	0.81[EUR][1000 genomes]
rs8053589	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv573285	chr16:79158182-80127326	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv906992	chr16:79649394-79769790	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv530714	chr16:79661581-79925435	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv833296	chr16:79692236-79889727	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv833297	chr16:79732501-79920419	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17689625	RP11-345M22.2	cis	Skin Sun Exposed Lower leg	GTEx
rs17689625	RP11-345M22.2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:79742000-79749400	Weak transcription	Pancreas	Pancrea
2	chr16:79742400-79749400	Weak transcription	Aorta	Aorta
3	chr16:79746200-79749800	Enhancers	Duodenum Mucosa	Duodenum
4	chr16:79746800-79749000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr16:79746800-79751600	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr16:79747000-79750600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr16:79747000-79751800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr16:79747800-79749000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr16:79747800-79750800	Enhancers	Ovary	ovary
10	chr16:79748000-79750000	Enhancers	Fetal Kidney	kidney
11	chr16:79748000-79756200	Weak transcription	Gastric	stomach
12	chr16:79748200-79749000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr16:79748200-79760400	Enhancers	Fetal Intestine Small	intestine
14	chr16:79748400-79749000	Enhancers	Colon Smooth Muscle	Colon
15	chr16:79748400-79749200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr16:79748400-79749800	Enhancers	Liver	Liver
17	chr16:79748400-79752200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr16:79748400-79752200	Enhancers	Fetal Lung	lung
19	chr16:79748400-79752400	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr16:79748400-79760800	Enhancers	Fetal Intestine Large	intestine
21	chr16:79748600-79749000	Enhancers	Brain Germinal Matrix	brain
22	chr16:79748600-79749800	Enhancers	Stomach Mucosa	stomach
23	chr16:79748600-79750400	Weak transcription	Fetal Muscle Leg	muscle
24	chr16:79748800-79749600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr16:79748800-79749600	Enhancers	Pancreatic Islets	Pancreatic Islet

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