Variant report

Variant	rs6540580
Chromosome Location	chr1:210285936-210285937
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 170 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:160)

rs_ID	r²[population]
rs1028325	0.81[EUR][1000 genomes]
rs1040423	0.81[EUR][1000 genomes]
rs10746423	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10779516	0.91[EUR][1000 genomes]
rs10779517	0.92[EUR][1000 genomes]
rs10779518	0.92[EUR][1000 genomes]
rs10779523	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10779525	0.84[AMR][1000 genomes]
rs10863811	0.90[EUR][1000 genomes]
rs1099863	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11119370	0.84[EUR][1000 genomes]
rs11119374	0.86[EUR][1000 genomes]
rs11119375	0.83[EUR][1000 genomes]
rs11119376	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11119382	0.88[EUR][1000 genomes]
rs11119407	0.89[EUR][1000 genomes]
rs11119409	0.93[EUR][1000 genomes]
rs11119413	0.91[EUR][1000 genomes]
rs11119414	0.92[EUR][1000 genomes]
rs11119425	0.89[AMR][1000 genomes]
rs11119427	0.86[AMR][1000 genomes]
rs11119428	0.86[AMR][1000 genomes]
rs11119429	0.84[AMR][1000 genomes]
rs12042135	0.93[EUR][1000 genomes]
rs12129172	0.86[AMR][1000 genomes]
rs126277	0.92[EUR][1000 genomes]
rs126278	0.87[EUR][1000 genomes]
rs1334567	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1334568	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1334569	0.95[EUR][1000 genomes]
rs1387933	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1387934	0.89[EUR][1000 genomes]
rs1413695	0.89[AMR][1000 genomes]
rs1490419	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs170552	0.89[EUR][1000 genomes]
rs170553	0.89[EUR][1000 genomes]
rs170555	0.89[EUR][1000 genomes]
rs170557	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs170558	0.89[EUR][1000 genomes]
rs183450	0.88[EUR][1000 genomes]
rs189000	0.89[EUR][1000 genomes]
rs189001	0.89[EUR][1000 genomes]
rs1933477	0.83[AMR][1000 genomes]
rs2046849	0.92[EUR][1000 genomes]
rs2142861	0.86[EUR][1000 genomes]
rs2200970	0.92[EUR][1000 genomes]
rs2205987	0.89[EUR][1000 genomes]
rs2205988	0.92[EUR][1000 genomes]
rs2205989	0.86[EUR][1000 genomes]
rs227168	0.88[EUR][1000 genomes]
rs227169	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs227170	0.88[EUR][1000 genomes]
rs227171	0.88[EUR][1000 genomes]
rs227172	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs227173	0.89[EUR][1000 genomes]
rs227174	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs227175	0.89[EUR][1000 genomes]
rs227176	0.89[EUR][1000 genomes]
rs227177	0.89[EUR][1000 genomes]
rs227178	0.88[EUR][1000 genomes]
rs227179	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs227181	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs227182	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs227183	0.89[EUR][1000 genomes]
rs227184	0.89[EUR][1000 genomes]
rs227186	0.89[EUR][1000 genomes]
rs227187	0.89[EUR][1000 genomes]
rs227188	0.89[EUR][1000 genomes]
rs227190	0.89[EUR][1000 genomes]
rs227191	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs227193	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs227195	0.89[EUR][1000 genomes]
rs227196	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs227197	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs227200	0.89[EUR][1000 genomes]
rs227201	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs227202	0.89[EUR][1000 genomes]
rs227203	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs227204	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs227205	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs227206	0.87[EUR][1000 genomes]
rs227207	0.90[EUR][1000 genomes]
rs227209	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs227211	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs227216	0.89[EUR][1000 genomes]
rs227217	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs227218	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs227219	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs227221	0.89[EUR][1000 genomes]
rs227223	0.89[EUR][1000 genomes]
rs227224	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs227225	0.84[EUR][1000 genomes]
rs227226	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs227227	0.89[EUR][1000 genomes]
rs227228	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs227229	0.89[EUR][1000 genomes]
rs227230	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs227232	0.89[EUR][1000 genomes]
rs2357212	0.86[EUR][1000 genomes]
rs2473073	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2485890	0.83[AMR][1000 genomes]
rs2485891	0.84[AMR][1000 genomes]
rs2485892	0.84[AMR][1000 genomes]
rs2494168	0.84[AMR][1000 genomes]
rs2494169	0.84[AMR][1000 genomes]
rs2494189	0.84[AMR][1000 genomes]
rs2494190	0.86[AMR][1000 genomes]
rs2636373	0.89[EUR][1000 genomes]
rs2636376	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2743889	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2743891	0.89[EUR][1000 genomes]
rs4421592	0.87[AMR][1000 genomes]
rs4462143	0.81[EUR][1000 genomes]
rs4844947	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4844948	0.91[EUR][1000 genomes]
rs6540569	0.85[EUR][1000 genomes]
rs6540573	0.92[EUR][1000 genomes]
rs6540575	0.81[EUR][1000 genomes]
rs6540584	0.86[AMR][1000 genomes]
rs6656855	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6657984	0.88[EUR][1000 genomes]
rs6667057	0.81[EUR][1000 genomes]
rs6678081	0.81[EUR][1000 genomes]
rs6682334	0.89[EUR][1000 genomes]
rs6682546	0.80[EUR][1000 genomes]
rs6689456	0.88[EUR][1000 genomes]
rs6702257	0.89[EUR][1000 genomes]
rs6702961	0.81[EUR][1000 genomes]
rs701947	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs701948	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7513171	0.89[EUR][1000 genomes]
rs7514257	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7519750	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7525980	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7528647	0.87[EUR][1000 genomes]
rs7530426	0.92[EUR][1000 genomes]
rs7541569	0.82[AMR][1000 genomes]
rs7544033	0.87[EUR][1000 genomes]
rs7547709	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7548989	0.87[EUR][1000 genomes]
rs846545	0.89[EUR][1000 genomes]
rs846546	0.81[EUR][1000 genomes]
rs846548	0.90[EUR][1000 genomes]
rs846549	0.89[EUR][1000 genomes]
rs846550	0.89[EUR][1000 genomes]
rs846551	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs846552	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs846553	0.89[EUR][1000 genomes]
rs846554	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs846555	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs846556	0.89[EUR][1000 genomes]
rs846557	0.89[EUR][1000 genomes]
rs846559	0.89[EUR][1000 genomes]
rs860155	0.81[EUR][1000 genomes]
rs9429827	0.81[EUR][1000 genomes]
rs9430024	0.86[EUR][1000 genomes]
rs9430026	0.86[EUR][1000 genomes]
rs9659395	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9662387	0.86[EUR][1000 genomes]
rs986057	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv873140	chr1:210068117-210335644	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv1821002	chr1:210108473-210291476	ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv873141	chr1:210228131-210296910	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv873142	chr1:210233610-210291121	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv873143	chr1:210233610-210296910	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv873144	chr1:210252522-210347417	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv818800	chr1:210258653-210304319	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv3452678	chr1:210284385-210289804	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
10	esv3452679	chr1:210284385-210289804	Enhancers Weak transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210268400-210287400	Weak transcription	Brain Germinal Matrix	brain
2	chr1:210274200-210290600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:210280000-210290600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:210283000-210298000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:210285400-210286400	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
6	chr1:210285400-210288400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
7	chr1:210285600-210288000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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