Variant report

Variant	rs10913118
Chromosome Location	chr1:175954755-175954756
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10494495	0.91[JPT][hapmap]
rs10753117	0.86[JPT][hapmap]
rs10798425	0.91[JPT][hapmap]
rs10798434	0.91[JPT][hapmap]
rs10798442	0.86[JPT][hapmap]
rs10798445	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs10798446	0.82[JPT][hapmap]
rs10913117	0.91[JPT][hapmap]
rs10913135	0.81[JPT][hapmap]
rs10913137	0.82[JPT][hapmap]
rs10913143	0.82[JPT][hapmap]
rs10913144	0.82[JPT][hapmap]
rs10913147	0.82[JPT][hapmap]
rs11810706	0.95[CEU][hapmap];0.91[JPT][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes]
rs12029090	0.84[JPT][hapmap]
rs12033847	0.86[JPT][hapmap]
rs12049077	0.82[JPT][hapmap]
rs12135395	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12138008	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12404596	0.86[JPT][hapmap]
rs12723724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12729524	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12741940	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12756741	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16849486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17354120	0.82[JPT][hapmap]
rs2481628	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap]
rs2481630	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs2481631	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.85[YRI][hapmap]
rs2481633	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs2481646	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2481655	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2487144	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap]
rs2502823	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2502829	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2502831	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap]
rs2502845	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs34973462	0.90[EUR][1000 genomes]
rs3934392	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4409605	0.91[JPT][hapmap]
rs520661	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs617078	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs6660080	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6665385	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6678628	0.82[JPT][hapmap]
rs6678812	0.82[JPT][hapmap]
rs6682194	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6697860	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap]
rs704829	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7517503	0.82[JPT][hapmap]
rs7530719	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7549160	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs791743	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap]
rs791751	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap]
rs791753	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs9425447	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1823794	chr1:175869554-176311778	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv872561	chr1:175949646-176092167	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv872562	chr1:175949646-176141866	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv872563	chr1:175949646-176184625	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10913118	VAMP4	cis	parietal	SCAN
rs10913118	EME2	trans	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175904200-175956200	Weak transcription	Psoas Muscle	Psoas
2	chr1:175906400-175962600	Weak transcription	NH-A	brain
3	chr1:175908000-175959400	Weak transcription	NHEK	skin
4	chr1:175946000-175996000	Weak transcription	HMEC	breast
5	chr1:175948200-175957400	Weak transcription	Brain Substantia Nigra	brain
6	chr1:175948200-175961400	Weak transcription	NHLF	lung
7	chr1:175949200-175958600	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr1:175949200-175958600	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr1:175949400-175957000	Weak transcription	Osteobl	bone
10	chr1:175949600-175954800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:175949800-175954800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:175950000-175961200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:175950200-175955400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:175950200-175956400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:175950400-175954800	ZNF genes & repeats	Primary B cells from cord blood	blood
16	chr1:175950400-175955000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
17	chr1:175950400-175955000	ZNF genes & repeats	GM12878-XiMat	blood
18	chr1:175950600-175954800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
19	chr1:175951000-175955000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:175951200-175957600	Strong transcription	HSMM	muscle
21	chr1:175951400-175954800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
22	chr1:175951600-175956200	Strong transcription	Hela-S3	cervix
23	chr1:175951600-175958600	Weak transcription	Fetal Heart	heart
24	chr1:175951800-175954800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr1:175951800-175954800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:175951800-175954800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
27	chr1:175951800-175955000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
28	chr1:175951800-175956000	Strong transcription	Skeletal Muscle Female	skeletal muscle
29	chr1:175952000-175955000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
30	chr1:175952000-175958000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr1:175952400-175954800	ZNF genes & repeats	Thymus	Thymus
32	chr1:175952400-175955000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr1:175952600-175958800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr1:175952800-175954800	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
35	chr1:175952800-175954800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr1:175952800-175954800	Strong transcription	Brain Anterior Caudate	brain
37	chr1:175953000-175954800	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 2	blood
38	chr1:175953000-175958000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr1:175953000-175958200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
40	chr1:175953200-175954800	Strong transcription	Fetal Lung	lung
41	chr1:175953200-175960000	Weak transcription	Fetal Brain Male	brain
42	chr1:175953400-175954800	Genic enhancers	Fetal Intestine Large	intestine
43	chr1:175953400-175957400	Strong transcription	NHDF-Ad	bronchial
44	chr1:175953600-175954800	Strong transcription	Fetal Muscle Leg	muscle
45	chr1:175953600-175954800	ZNF genes & repeats	Dnd41	blood
46	chr1:175953600-175958600	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr1:175953600-175960800	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr1:175953800-175954800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr1:175953800-175954800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr1:175953800-175954800	Enhancers	Stomach Mucosa	stomach

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