Variant report

Variant	rs10913117
Chromosome Location	chr1:175952208-175952209
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10218714	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10436856	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10494495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10753112	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.99[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753117	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10753118	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10798422	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10798425	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10798428	0.88[YRI][hapmap]
rs10798434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798442	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10798444	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10798445	0.85[JPT][hapmap]
rs10798446	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.87[YRI][hapmap]
rs10913116	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10913118	0.91[JPT][hapmap]
rs10913120	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10913124	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10913128	0.94[GIH][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs10913131	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10913132	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10913135	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap]
rs10913137	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.88[YRI][hapmap]
rs10913143	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.88[YRI][hapmap]
rs10913144	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap]
rs10913147	0.96[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap]
rs11810706	0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs12023976	0.85[EUR][1000 genomes]
rs12029090	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12033847	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12033976	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12040241	0.94[GIH][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap]
rs12049077	0.96[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap]
rs12066926	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12404596	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12723724	0.90[JPT][hapmap]
rs12729524	0.81[JPT][hapmap]
rs12735810	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16849486	0.91[JPT][hapmap]
rs17351562	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17354120	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap]
rs2481628	0.86[JPT][hapmap]
rs2481630	0.86[JPT][hapmap]
rs2481631	0.85[JPT][hapmap]
rs2481633	0.86[JPT][hapmap]
rs2481641	0.83[ASW][hapmap]
rs2481655	0.81[JPT][hapmap]
rs2487144	0.86[JPT][hapmap]
rs2502823	0.81[JPT][hapmap]
rs2502831	0.86[JPT][hapmap]
rs2502834	0.83[ASW][hapmap];0.88[YRI][hapmap]
rs2502835	0.88[YRI][hapmap]
rs2502845	0.90[JPT][hapmap]
rs34973462	0.81[ASN][1000 genomes]
rs35846379	0.82[EUR][1000 genomes]
rs3748618	0.94[GIH][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap]
rs4409605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs520661	0.86[JPT][hapmap]
rs617078	0.86[JPT][hapmap]
rs6665385	0.86[JPT][hapmap]
rs6678628	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs6678812	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6680839	0.88[ASN][1000 genomes]
rs6687043	0.81[YRI][hapmap]
rs6688898	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6693299	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6697860	0.85[JPT][hapmap]
rs6703511	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs704829	0.86[JPT][hapmap]
rs7515914	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7517503	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap]
rs7527463	0.84[AFR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7534058	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7534948	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7539247	0.83[ASW][hapmap]
rs7549160	0.81[JPT][hapmap]
rs791751	0.86[JPT][hapmap]
rs791753	0.84[JPT][hapmap]
rs9425447	0.85[JPT][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
rs10913117	DARS2	cis	parietal	SCAN
rs10913117	PIGC	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175897000-175953000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr1:175897600-175953200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:175897800-175952400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:175898600-175953200	Weak transcription	Pancreas	Pancrea
5	chr1:175899200-175953200	Weak transcription	Esophagus	oesophagus
6	chr1:175904200-175956200	Weak transcription	Psoas Muscle	Psoas
7	chr1:175904600-175953000	Weak transcription	Right Ventricle	heart
8	chr1:175906400-175952400	Weak transcription	Spleen	Spleen
9	chr1:175906400-175962600	Weak transcription	NH-A	brain
10	chr1:175908000-175959400	Weak transcription	NHEK	skin
11	chr1:175917600-175953000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr1:175924600-175953200	Weak transcription	Gastric	stomach
13	chr1:175924600-175953200	Weak transcription	HepG2	liver
14	chr1:175940400-175953800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr1:175941000-175952600	Weak transcription	Colonic Mucosa	Colon
16	chr1:175941000-175953200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr1:175941200-175952400	Weak transcription	Left Ventricle	heart
18	chr1:175941200-175952400	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr1:175941200-175952400	Weak transcription	Thymus	Thymus
20	chr1:175941200-175952800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr1:175941200-175953200	Weak transcription	Lung	lung
22	chr1:175945000-175952400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr1:175945800-175953400	Weak transcription	Aorta	Aorta
24	chr1:175946000-175996000	Weak transcription	HMEC	breast
25	chr1:175947600-175952800	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr1:175948200-175952400	Weak transcription	Brain Hippocampus Middle	brain
27	chr1:175948200-175952800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr1:175948200-175957400	Weak transcription	Brain Substantia Nigra	brain
29	chr1:175948200-175961400	Weak transcription	NHLF	lung
30	chr1:175948400-175952400	Weak transcription	Fetal Stomach	stomach
31	chr1:175948400-175953400	Weak transcription	Colon Smooth Muscle	Colon
32	chr1:175948600-175953400	Weak transcription	HUVEC	blood vessel
33	chr1:175948800-175952400	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr1:175949200-175953400	Strong transcription	Primary T cells from cord blood	blood
35	chr1:175949200-175958600	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr1:175949200-175958600	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr1:175949400-175957000	Weak transcription	Osteobl	bone
38	chr1:175949600-175954800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:175949800-175952400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr1:175949800-175954800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr1:175950000-175952400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr1:175950000-175952600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:175950000-175952800	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr1:175950000-175954000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:175950000-175954200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:175950000-175961200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr1:175950200-175952400	Strong transcription	HSMMtube	muscle
48	chr1:175950200-175952800	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr1:175950200-175953000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:175950200-175955400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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