Variant report

Variant	rs1502340
Chromosome Location	chr1:45600970-45600971
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs17394390	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17397799	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1938299	1.00[AFR][1000 genomes]
rs2096435	1.00[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4660298	1.00[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4660837	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660838	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660840	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788378	1.00[AFR][1000 genomes]
rs61788379	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61788380	1.00[AFR][1000 genomes]
rs61788382	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61788383	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61788386	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61788387	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788388	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788390	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788393	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788427	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61788428	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61788429	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788430	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788436	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788438	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788439	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788440	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788441	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788447	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788449	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788455	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61789766	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61789768	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61789773	0.93[AMR][1000 genomes]
rs61789774	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs61789775	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61789777	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61789778	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61789782	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs61789785	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs61789788	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61789789	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61789808	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs61789809	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs61789814	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs61789816	1.00[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs61789817	1.00[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs61789818	1.00[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs61789819	1.00[AFR][1000 genomes]
rs61789822	1.00[AFR][1000 genomes]
rs61789826	1.00[AFR][1000 genomes]
rs61789830	1.00[AFR][1000 genomes]
rs61789957	1.00[AFR][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	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
2	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
3	nsv915644	chr1:45282802-45696079	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
5	nsv546148	chr1:45500294-45627663	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45590000-45627000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:45600200-45601000	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr1:45600200-45601000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:45600200-45601000	Enhancers	Liver	Liver
5	chr1:45600200-45601000	Enhancers	Brain Substantia Nigra	brain
6	chr1:45600200-45601000	Enhancers	Sigmoid Colon	Sigmoid Colon
7	chr1:45600200-45601200	Enhancers	Brain Anterior Caudate	brain
8	chr1:45600200-45601200	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr1:45600200-45601600	Enhancers	Fetal Intestine Small	intestine
10	chr1:45600200-45601800	Enhancers	Fetal Intestine Large	intestine
11	chr1:45600400-45601000	Enhancers	Fetal Lung	lung
12	chr1:45600400-45601200	Enhancers	Fetal Kidney	kidney
13	chr1:45600400-45605000	Enhancers	HepG2	liver
14	chr1:45600600-45601000	Enhancers	Pancreatic Islets	Pancreatic Islet
15	chr1:45600600-45601600	Weak transcription	Small Intestine	intestine
16	chr1:45600600-45606400	Weak transcription	Ovary	ovary
17	chr1:45600800-45601600	Enhancers	Duodenum Mucosa	Duodenum
18	chr1:45600800-45606200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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