Variant report

Variant	rs10753112
Chromosome Location	chr1:175958987-175958988
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10218714	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10436856	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10494495	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10753117	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10753118	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10798422	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10798425	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10798428	0.88[YRI][hapmap]
rs10798434	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798442	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10798444	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10798446	0.96[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.87[YRI][hapmap]
rs10913116	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10913117	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]
rs10913120	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10913124	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10913128	0.97[GIH][hapmap];0.83[TSI][hapmap]
rs10913131	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10913132	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10913133	0.81[AMR][1000 genomes]
rs10913134	0.81[AMR][1000 genomes]
rs10913135	0.95[CEU][hapmap];0.84[CHB][hapmap];0.87[YRI][hapmap];0.81[AMR][1000 genomes]
rs10913137	0.96[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes]
rs10913143	0.96[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.88[YRI][hapmap]
rs10913144	0.96[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.84[YRI][hapmap]
rs10913147	0.92[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap]
rs11810706	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs12023976	0.84[EUR][1000 genomes]
rs12029090	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12033847	0.88[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.96[TSI][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12033976	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12040241	0.97[GIH][hapmap];0.83[TSI][hapmap]
rs12047295	0.85[JPT][hapmap]
rs12049077	0.92[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap]
rs12066926	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12404596	0.88[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.96[TSI][hapmap];0.84[YRI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12735810	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17351562	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17354120	0.94[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.99[MKK][hapmap];0.96[TSI][hapmap];0.84[YRI][hapmap]
rs2481641	0.83[ASW][hapmap]
rs2502834	0.83[ASW][hapmap];0.88[YRI][hapmap]
rs2502835	0.88[YRI][hapmap]
rs2502845	0.82[JPT][hapmap]
rs34973462	0.81[ASN][1000 genomes]
rs35846379	0.83[EUR][1000 genomes]
rs3748618	0.97[GIH][hapmap];0.83[TSI][hapmap]
rs4409605	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6678628	0.96[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs6678812	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs6680839	0.88[ASN][1000 genomes]
rs6687043	0.81[YRI][hapmap]
rs6688898	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6693299	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6703511	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7515914	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7517503	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.98[LWK][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.88[YRI][hapmap]
rs7522843	0.81[AMR][1000 genomes]
rs7527463	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7534058	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7534948	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7539247	0.83[ASW][hapmap]
rs7553759	0.80[AMR][1000 genomes]

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

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175906400-175962600	Weak transcription	NH-A	brain
2	chr1:175908000-175959400	Weak transcription	NHEK	skin
3	chr1:175946000-175996000	Weak transcription	HMEC	breast
4	chr1:175948200-175961400	Weak transcription	NHLF	lung
5	chr1:175950000-175961200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:175953200-175960000	Weak transcription	Fetal Brain Male	brain
7	chr1:175953600-175960800	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr1:175953800-175959000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:175953800-175959000	Weak transcription	HUVEC	blood vessel
10	chr1:175953800-175961000	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr1:175953800-175962000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:175953800-175999600	Weak transcription	Colonic Mucosa	Colon
13	chr1:175954000-175959000	Weak transcription	Aorta	Aorta
14	chr1:175954000-175959000	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr1:175954000-175959400	Weak transcription	Spleen	Spleen
16	chr1:175954000-175959600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:175954000-175959800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:175954000-175960000	Weak transcription	Fetal Stomach	stomach
19	chr1:175954000-175960200	Weak transcription	Gastric	stomach
20	chr1:175954000-175960200	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr1:175954000-175961000	Weak transcription	Esophagus	oesophagus
22	chr1:175954000-175962000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:175954000-175962000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr1:175954000-175963600	Weak transcription	Lung	lung
25	chr1:175954000-175977800	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr1:175954000-175978000	Weak transcription	Left Ventricle	heart
27	chr1:175954000-175987800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:175954200-175959200	Weak transcription	Fetal Muscle Trunk	muscle
29	chr1:175954200-175960600	Weak transcription	Colon Smooth Muscle	Colon
30	chr1:175954200-175961600	Weak transcription	Brain Hippocampus Middle	brain
31	chr1:175954200-175962000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr1:175954400-175959000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr1:175954400-175959800	Weak transcription	Brain Germinal Matrix	brain
34	chr1:175954600-175960400	Weak transcription	A549	lung
35	chr1:175954600-175964600	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr1:175954800-175959200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:175954800-175959400	Weak transcription	Thymus	Thymus
38	chr1:175954800-175961000	Strong transcription	Primary B cells from cord blood	blood
39	chr1:175954800-175961000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr1:175954800-175961800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr1:175954800-175962200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr1:175954800-175963000	Weak transcription	Brain Anterior Caudate	brain
43	chr1:175954800-175968600	Weak transcription	Fetal Muscle Leg	muscle
44	chr1:175955000-175959200	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr1:175955000-175959800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr1:175955000-175960600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr1:175955000-175962000	Weak transcription	Fetal Intestine Small	intestine
48	chr1:175955000-175962200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr1:175955000-175963800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr1:175955400-175959400	Strong transcription	Primary hematopoietic stem cells	blood

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