Variant report

Variant	rs2502823
Chromosome Location	chr1:176038749-176038750
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10494495	0.82[JPT][hapmap]
rs10753117	0.86[JPT][hapmap]
rs10798425	0.81[JPT][hapmap]
rs10798434	0.82[JPT][hapmap]
rs10798442	0.87[JPT][hapmap]
rs10798445	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs10798446	0.83[JPT][hapmap]
rs10913117	0.81[JPT][hapmap]
rs10913118	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]
rs10913135	0.82[JPT][hapmap]
rs10913137	0.83[JPT][hapmap]
rs10913143	0.83[JPT][hapmap]
rs10913144	0.83[JPT][hapmap]
rs10913147	0.83[JPT][hapmap]
rs11810706	0.95[CEU][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes]
rs12029090	0.85[JPT][hapmap]
rs12033847	0.86[JPT][hapmap]
rs12049077	0.83[JPT][hapmap]
rs12135395	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12138008	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12404596	0.86[JPT][hapmap]
rs12723724	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12729524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12741940	0.82[AMR][1000 genomes]
rs12756741	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16849486	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17354120	0.82[JPT][hapmap]
rs1974142	0.84[EUR][1000 genomes]
rs2039230	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap]
rs2175177	0.85[JPT][hapmap]
rs2457418	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs2481628	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs2481630	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs2481631	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes]
rs2481633	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs2481646	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2481655	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]
rs2481658	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2481662	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2487144	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2502829	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2502831	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs2502845	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs34973462	0.87[EUR][1000 genomes]
rs3934392	0.82[AMR][1000 genomes]
rs3962371	0.82[CEU][hapmap]
rs4409605	0.82[JPT][hapmap]
rs513354	0.81[EUR][1000 genomes]
rs520661	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs617078	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs6660080	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6665385	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6678628	0.83[JPT][hapmap]
rs6678812	0.82[JPT][hapmap]
rs668154	0.81[EUR][1000 genomes]
rs6682194	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6697860	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs679728	0.86[CEU][hapmap];0.81[JPT][hapmap]
rs704829	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs704834	0.86[CEU][hapmap];0.81[JPT][hapmap]
rs7517503	0.82[JPT][hapmap]
rs7530719	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7535769	0.86[CEU][hapmap];0.81[JPT][hapmap]
rs7549160	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[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]
rs791743	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs791751	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap]
rs791753	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs813180	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap]
rs9425447	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs944365	0.82[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	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
5	nsv872564	chr1:176027978-176102808	Enhancers Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175976800-176046000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr1:175978200-176050600	Weak transcription	Aorta	Aorta
3	chr1:175978400-176069000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr1:175979600-176045400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:175994200-176065200	Weak transcription	Psoas Muscle	Psoas
6	chr1:176004200-176039800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:176006000-176045200	Weak transcription	GM12878-XiMat	blood
8	chr1:176006200-176049000	Weak transcription	HSMM	muscle
9	chr1:176007800-176066400	Weak transcription	Fetal Brain Male	brain
10	chr1:176010200-176048000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr1:176010400-176066000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr1:176012200-176044800	Weak transcription	Fetal Stomach	stomach
13	chr1:176012200-176045200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr1:176012200-176045200	Weak transcription	Esophagus	oesophagus
15	chr1:176012200-176045200	Weak transcription	Fetal Lung	lung
16	chr1:176012400-176045400	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr1:176012400-176045800	Weak transcription	Brain Hippocampus Middle	brain
18	chr1:176012400-176048200	Weak transcription	Ovary	ovary
19	chr1:176012400-176048200	Weak transcription	Thymus	Thymus
20	chr1:176012400-176062800	Weak transcription	Lung	lung
21	chr1:176012400-176065800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:176012800-176040000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr1:176012800-176042600	Weak transcription	Liver	Liver
24	chr1:176012800-176047000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr1:176013000-176040000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr1:176013000-176045000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:176013400-176040000	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr1:176013600-176040000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:176014400-176039800	Weak transcription	Primary B cells from peripheral blood	blood
30	chr1:176014400-176045200	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr1:176015400-176039000	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr1:176015400-176040200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:176015600-176040000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:176021600-176045000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:176022800-176039800	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr1:176024400-176039800	Weak transcription	Primary B cells from cord blood	blood
37	chr1:176028000-176045400	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr1:176028200-176045400	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr1:176028200-176048200	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr1:176028200-176079200	Weak transcription	HSMMtube	muscle
41	chr1:176028400-176042600	Weak transcription	Brain Angular Gyrus	brain
42	chr1:176028400-176047200	Weak transcription	A549	lung
43	chr1:176028400-176047800	Weak transcription	Hela-S3	cervix
44	chr1:176028400-176049600	Weak transcription	K562	blood
45	chr1:176028800-176047200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr1:176029000-176040000	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr1:176029600-176048000	Weak transcription	HepG2	liver
48	chr1:176030000-176047400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr1:176030600-176045600	Weak transcription	Primary hematopoietic stem cells	blood
50	chr1:176030800-176048200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links