Variant report

Variant	rs11718165
Chromosome Location	chr3:49696797-49696798
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49689149..49690759-chr3:49696566..49699118,2	MCF-7	breast:
2	chr3:49679483..49683114-chr3:49694682..49696978,3	MCF-7	breast:
3	chr3:49683730..49686310-chr3:49694623..49697344,2	K562	blood:
4	chr3:49696156..49697699-chr3:49699685..49702329,2	K562	blood:
5	chr3:49686939..49689819-chr3:49694987..49697482,3	K562	blood:
6	chr3:49599138..49600708-chr3:49694721..49696847,2	K562	blood:
7	chr3:49692557..49695164-chr3:49696154..49698267,2	K562	blood:

Variant related genes	Relation type
ENSG00000164061	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1050088	0.82[GIH][hapmap]
rs1060962	0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10865955	0.82[GIH][hapmap]
rs11130212	0.86[ASN][1000 genomes]
rs11130213	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1131095	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11709525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11710037	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11720597	0.82[AMR][1000 genomes]
rs11917431	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11919311	0.92[CHD][hapmap];0.85[GIH][hapmap]
rs11921590	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13064576	0.82[AMR][1000 genomes]
rs13085791	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13316695	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1352890	0.81[ASN][1000 genomes]
rs1568661	0.82[GIH][hapmap]
rs1801143	1.00[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs1873625	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1873626	0.81[ASN][1000 genomes]
rs2005557	0.91[ASN][1000 genomes]
rs2131104	0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2131109	0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2172252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2329020	0.92[CHD][hapmap];0.88[GIH][hapmap];0.81[ASN][1000 genomes]
rs3197999	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34762726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35007338	0.81[ASN][1000 genomes]
rs35404120	0.81[ASN][1000 genomes]
rs35701831	0.82[GIH][hapmap]
rs3811697	1.00[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap]
rs3870338	0.82[GIH][hapmap]
rs3924462	0.82[GIH][hapmap]
rs4283605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4625	1.00[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs4855839	0.82[GIH][hapmap]
rs4855847	0.81[ASN][1000 genomes]
rs4855852	0.92[CHD][hapmap];0.85[GIH][hapmap]
rs4855859	0.82[GIH][hapmap]
rs4855864	0.82[GIH][hapmap]
rs4855881	0.92[CHD][hapmap];0.88[GIH][hapmap]
rs4855883	0.85[ASN][1000 genomes]
rs4855884	1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6765869	0.91[ASN][1000 genomes]
rs6766131	1.00[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs6770670	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6803222	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7614725	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7622302	0.83[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap]
rs7633271	1.00[CEU][hapmap]
rs7637999	0.82[GIH][hapmap]
rs885592	0.82[GIH][hapmap]
rs9811982	1.00[CEU][hapmap]
rs9812791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9822268	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9823546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9824092	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9827021	1.00[CEU][hapmap]
rs9827708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9833611	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9836291	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9837027	1.00[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs9837341	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9837520	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9853683	1.00[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs9858213	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap]
rs9858280	1.00[CEU][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs9858542	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];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862080	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9875617	1.00[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes]
rs9882740	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][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	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1011428	chr3:49649989-49706068	Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
4	esv1825898	chr3:49688948-49764849	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	esv1808511	chr3:49689880-49744825	Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs11718165	RNF123	cis	parietal	SCAN
rs11718165	GPX1	cis	parietal	SCAN
rs11718165	FAM212A	cis	Muscle Skeletal	GTEx
rs11718165	RBM6	cis	cerebellum	SCAN
rs11718165	C3orf62	cis	multi-tissue	Pritchard
rs11718165	CISH	cis	lymphoblastoid	seeQTL
rs11718165	USP4	cis	multi-tissue	Pritchard
rs11718165	ZNF589	cis	parietal	SCAN
rs11718165	IP6K2	cis	cerebellum	SCAN
rs11718165	DAG1	cis	multi-tissue	Pritchard
rs11718165	PARP3	cis	parietal	SCAN
rs11718165	RNF123	cis	cerebellum	SCAN
rs11718165	MST1	cis	brain	seeQTL
rs11718165	HSS00328072	cis	multi-tissue	Pritchard
rs11718165	NBEAL2	cis	cerebellum	SCAN
rs11718165	MST1	cis	Liver	GTEx
rs11718165	MYL3	cis	parietal	SCAN
rs11718165	MST1	cis	multi-tissue	Pritchard

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49685200-49708200	Strong transcription	Brain Germinal Matrix	brain
2	chr3:49685400-49708400	Strong transcription	Fetal Brain Female	brain
3	chr3:49686600-49697200	Weak transcription	Pancreas	Pancrea
4	chr3:49686600-49710600	Weak transcription	Right Atrium	heart
5	chr3:49687600-49702400	Weak transcription	Right Ventricle	heart
6	chr3:49687600-49705800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr3:49690400-49702000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:49690400-49710600	Weak transcription	Brain Substantia Nigra	brain
9	chr3:49692200-49710400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:49692400-49700800	Weak transcription	Brain Anterior Caudate	brain
11	chr3:49693200-49703200	Weak transcription	Gastric	stomach
12	chr3:49693400-49698600	Weak transcription	Spleen	Spleen
13	chr3:49693600-49696800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
14	chr3:49694000-49698000	Weak transcription	Brain Hippocampus Middle	brain
15	chr3:49694200-49698600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr3:49694600-49697400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr3:49694800-49698800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:49695000-49702000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr3:49695200-49710600	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr3:49695600-49697200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:49695800-49704000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:49696200-49700800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr3:49696400-49700400	Weak transcription	Brain Angular Gyrus	brain
24	chr3:49696600-49698800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr3:49696600-49701400	Weak transcription	HepG2	liver
26	chr3:49696600-49701800	Weak transcription	Fetal Muscle Leg	muscle

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