Variant report

Variant	rs520661
Chromosome Location	chr1:176129276-176129277
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10494495	0.86[JPT][hapmap]
rs10753117	0.91[JPT][hapmap]
rs10798425	0.86[JPT][hapmap]
rs10798434	0.86[JPT][hapmap]
rs10798442	0.91[JPT][hapmap]
rs10798445	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10798446	0.87[JPT][hapmap]
rs10913117	0.86[JPT][hapmap]
rs10913118	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs10913135	0.86[JPT][hapmap]
rs10913137	0.87[JPT][hapmap]
rs10913143	0.87[JPT][hapmap]
rs10913144	0.87[JPT][hapmap]
rs10913147	0.87[JPT][hapmap]
rs10913152	0.87[AMR][1000 genomes]
rs10913166	0.82[AMR][1000 genomes]
rs11810706	0.95[CEU][hapmap];0.86[JPT][hapmap]
rs12029090	0.90[JPT][hapmap]
rs12033847	0.91[JPT][hapmap]
rs12049077	0.87[JPT][hapmap]
rs12117377	0.88[AMR][1000 genomes]
rs12138008	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs12404596	0.91[JPT][hapmap]
rs12723724	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs12729524	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes]
rs12758275	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16849486	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs17354120	0.86[JPT][hapmap]
rs1858537	0.88[AMR][1000 genomes]
rs191606	0.85[CEU][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes]
rs1974142	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2039230	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2102479	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2175177	0.90[JPT][hapmap]
rs2175178	0.88[AMR][1000 genomes]
rs2455730	0.87[AMR][1000 genomes]
rs2455732	0.87[AMR][1000 genomes]
rs2455749	0.88[AMR][1000 genomes]
rs2455762	0.84[AMR][1000 genomes]
rs2455764	0.80[AMR][1000 genomes]
rs2457418	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2481628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2481630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2481631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2481633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2481646	0.82[EUR][1000 genomes]
rs2481655	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs2481662	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2487144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2502823	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs2502829	0.81[EUR][1000 genomes]
rs2502831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2502845	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2504501	0.87[AMR][1000 genomes]
rs35907544	0.88[AMR][1000 genomes]
rs3962371	0.86[CEU][hapmap];0.83[JPT][hapmap];0.88[AMR][1000 genomes]
rs4298694	0.88[AMR][1000 genomes]
rs4409605	0.86[JPT][hapmap]
rs482228	0.85[AMR][1000 genomes]
rs501142	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs513354	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs534088	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs542742	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs596859	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs617078	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs659279	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6665385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6678628	0.87[JPT][hapmap]
rs6678812	0.86[JPT][hapmap]
rs668154	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6687280	0.85[AMR][1000 genomes]
rs6697860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6700932	0.88[AMR][1000 genomes]
rs670143	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs679728	0.90[CEU][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs704829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs704834	0.90[CEU][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs71645275	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7517503	0.86[JPT][hapmap]
rs7535769	0.90[CEU][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes]
rs7549160	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs791743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs791746	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs791747	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs791750	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs791751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs791752	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs791753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs813180	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9425447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs944365	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[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	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	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
3	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
4	nsv548246	chr1:176043797-176136273	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv872565	chr1:176058782-176172795	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:176054400-176131600	Weak transcription	NH-A	brain
2	chr1:176055000-176141600	Weak transcription	Hela-S3	cervix
3	chr1:176065600-176154800	Weak transcription	Aorta	Aorta
4	chr1:176069000-176139200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:176069200-176138800	Weak transcription	HUVEC	blood vessel
6	chr1:176070400-176151400	Weak transcription	Pancreas	Pancrea
7	chr1:176072000-176140600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:176085400-176142400	Weak transcription	Lung	lung
9	chr1:176095600-176130200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr1:176096000-176138800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:176100800-176153200	Weak transcription	Colonic Mucosa	Colon
12	chr1:176102800-176130000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:176102800-176130600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr1:176108600-176129800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr1:176110600-176164000	Weak transcription	NHLF	lung
16	chr1:176111800-176139400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr1:176115800-176129600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:176116000-176146200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:176121200-176130800	Weak transcription	HepG2	liver
20	chr1:176122000-176130200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:176122000-176139800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:176123200-176130600	Weak transcription	Thymus	Thymus
23	chr1:176123800-176131200	Weak transcription	K562	blood
24	chr1:176123800-176139800	Weak transcription	Fetal Kidney	kidney
25	chr1:176123800-176144200	Weak transcription	Left Ventricle	heart
26	chr1:176123800-176150000	Weak transcription	Osteobl	bone
27	chr1:176125200-176131000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:176126000-176130400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:176126000-176132000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:176126400-176129400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr1:176126400-176129400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
32	chr1:176126400-176129800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:176126400-176130000	Weak transcription	Fetal Stomach	stomach
34	chr1:176126400-176130200	ZNF genes & repeats	GM12878-XiMat	blood
35	chr1:176126400-176168800	Weak transcription	Small Intestine	intestine
36	chr1:176126600-176129400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
37	chr1:176126800-176139800	Weak transcription	HSMMtube	muscle
38	chr1:176127000-176130000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr1:176127000-176147000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr1:176127000-176174000	Weak transcription	Colon Smooth Muscle	Colon
41	chr1:176127200-176130600	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr1:176127200-176137800	Weak transcription	HSMM	muscle
43	chr1:176127200-176153400	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr1:176127400-176139200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr1:176127400-176139600	Weak transcription	Brain Anterior Caudate	brain
46	chr1:176127400-176140200	Weak transcription	Brain Hippocampus Middle	brain
47	chr1:176127400-176141200	Weak transcription	HMEC	breast
48	chr1:176127400-176143200	Weak transcription	Brain Substantia Nigra	brain
49	chr1:176127400-176144200	Weak transcription	A549	lung
50	chr1:176127400-176153400	Weak transcription	Stomach Smooth Muscle	stomach

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