Variant report

Variant	rs2660301
Chromosome Location	chr1:98521585-98521586
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 146 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:138)

rs_ID	r²[population]
rs10747495	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10747496	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10783082	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10875121	0.84[ASN][1000 genomes]
rs10875125	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11165935	0.84[ASN][1000 genomes]
rs11165937	0.84[ASN][1000 genomes]
rs1198571	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1198572	0.93[ASN][1000 genomes]
rs1198573	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1198574	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1198575	1.00[ASN][1000 genomes]
rs1198576	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1198577	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1198578	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1198579	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1198580	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1198581	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1198582	1.00[ASN][1000 genomes]
rs1198583	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1198588	1.00[ASN][1000 genomes]
rs1198589	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1198590	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1198591	1.00[ASN][1000 genomes]
rs1198592	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1198593	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1198594	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1198596	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1198598	1.00[ASN][1000 genomes]
rs1198600	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1211661	0.97[ASN][1000 genomes]
rs1622611	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1628294	0.93[ASN][1000 genomes]
rs1702291	1.00[ASN][1000 genomes]
rs1702292	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1702293	0.93[ASN][1000 genomes]
rs1702294	0.93[ASN][1000 genomes]
rs1782810	0.93[ASN][1000 genomes]
rs1782811	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1782812	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1782813	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1782815	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1782818	1.00[ASN][1000 genomes]
rs1892549	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1892550	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1892551	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1892552	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1938558	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1938559	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1938560	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1938561	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1938562	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1938563	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1938564	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1938565	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1938566	0.86[ASN][1000 genomes]
rs1938567	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1938568	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1938569	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1938571	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1938572	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1938573	0.81[EUR][1000 genomes]
rs2022864	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2022865	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2154402	0.93[ASN][1000 genomes]
rs2154403	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2391873	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2391902	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2391903	0.93[ASN][1000 genomes]
rs2391904	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2391905	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2660298	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2660299	1.00[ASN][1000 genomes]
rs2660300	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2660304	0.93[ASN][1000 genomes]
rs2802525	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2802529	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2802530	1.00[ASN][1000 genomes]
rs2802531	1.00[ASN][1000 genomes]
rs2802532	1.00[ASN][1000 genomes]
rs2802533	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2802535	0.90[ASN][1000 genomes]
rs2802536	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28582591	0.84[ASN][1000 genomes]
rs28641479	0.84[ASN][1000 genomes]
rs2893376	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41285694	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4245673	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4246516	0.84[ASN][1000 genomes]
rs4292998	0.93[ASN][1000 genomes]
rs4411173	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4447033	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4477335	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4480407	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs45522136	0.83[ASN][1000 genomes]
rs4573558	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4584446	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4634961	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4950117	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4950118	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4950119	0.93[ASN][1000 genomes]
rs4950120	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5005705	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61785881	0.84[ASN][1000 genomes]
rs61785883	0.84[ASN][1000 genomes]
rs61785886	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs61785888	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61786696	1.00[ASN][1000 genomes]
rs61786697	1.00[ASN][1000 genomes]
rs61789075	0.84[ASN][1000 genomes]
rs61789077	0.84[ASN][1000 genomes]
rs61789078	0.84[ASN][1000 genomes]
rs61789079	0.84[ASN][1000 genomes]
rs61789082	0.84[ASN][1000 genomes]
rs72963738	0.84[ASN][1000 genomes]
rs9285628	0.84[ASN][1000 genomes]
rs9324379	0.84[ASN][1000 genomes]
rs9324380	0.93[ASN][1000 genomes]
rs9324381	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9324382	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9324383	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9324384	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9324385	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9324386	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9324387	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9324388	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9324389	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9440288	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9440293	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9440393	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9658841	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9659380	0.84[ASN][1000 genomes]
rs9659624	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9659996	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9661157	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9724773	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9725319	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9727941	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012958	chr1:98081528-98864746	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv871625	chr1:98165091-98564736	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv871077	chr1:98274132-98541677	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
4	nsv1009621	chr1:98435638-98599284	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
5	nsv871230	chr1:98436232-98564736	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
6	nsv470729	chr1:98461443-98564736	Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
7	nsv546874	chr1:98461443-98564736	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
8	nsv830736	chr1:98488491-98663726	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:98520200-98522400	Weak transcription	Brain Anterior Caudate	brain
2	chr1:98520200-98522400	Weak transcription	Brain Hippocampus Middle	brain
3	chr1:98520200-98522400	Weak transcription	Brain Substantia Nigra	brain
4	chr1:98520400-98522200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:98520400-98524800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:98520400-98530000	Weak transcription	NHDF-Ad	bronchial
7	chr1:98520600-98522600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr1:98520800-98522000	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr1:98520800-98522200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr1:98520800-98522200	Weak transcription	Fetal Brain Male	brain
11	chr1:98520800-98522400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:98520800-98525000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:98521200-98521800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:98521200-98524400	Weak transcription	A549	lung
15	chr1:98521400-98521600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr1:98521400-98522200	Enhancers	Fetal Brain Female	brain
17	chr1:98521400-98525200	Weak transcription	HUVEC	blood vessel

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