Variant report

Variant	rs6702389
Chromosome Location	chr1:45546264-45546265
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11211075	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11211077	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11211080	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1143726	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1143727	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1144866	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1144867	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1144870	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1144871	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1152017	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1152018	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1152020	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1152022	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11585488	0.86[EUR][1000 genomes]
rs11588448	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1226722	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1226723	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1226727	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1226728	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1226736	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1226740	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1226749	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1226911	0.85[AMR][1000 genomes]
rs1226912	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12750360	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16832411	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1698295	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1938302	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1938406	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2211644	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2356304	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2883902	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2997400	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2997462	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3009973	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3009976	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3009978	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3121731	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3121770	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3128437	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3128443	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6429558	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6698681	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6700502	0.96[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs68139854	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7517524	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7528468	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7548075	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7552211	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv945917	chr1:45533650-45546555	Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Enhancers Bivalent/Poised TSS	TF binding region lncRNA	1 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	chr1:45525800-45558600	Weak transcription	HepG2	liver
2	chr1:45541000-45546800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:45543400-45555400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr1:45543600-45546800	ZNF genes & repeats	Fetal Brain Female	brain
5	chr1:45543800-45562200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr1:45544200-45546600	ZNF genes & repeats	Fetal Intestine Small	intestine
7	chr1:45544200-45546800	ZNF genes & repeats	Brain Germinal Matrix	brain
8	chr1:45544400-45549200	Weak transcription	Gastric	stomach
9	chr1:45544400-45550000	Weak transcription	Brain Hippocampus Middle	brain
10	chr1:45544400-45560200	Weak transcription	Pancreas	Pancrea
11	chr1:45544600-45552000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr1:45545000-45558200	Weak transcription	Duodenum Mucosa	Duodenum
13	chr1:45545800-45551400	Weak transcription	Fetal Stomach	stomach
14	chr1:45545800-45552000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr1:45546000-45549400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:45546000-45550600	Weak transcription	Aorta	Aorta
17	chr1:45546000-45554800	Weak transcription	Ovary	ovary

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