Variant report

Variant	rs10001162
Chromosome Location	chr4:87006350-87006351
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10009993	0.99[ASN][1000 genomes]
rs10023731	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10028075	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1010778	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10856856	0.89[ASN][1000 genomes]
rs11097091	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11097092	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11934691	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12502902	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12502934	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12512583	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12644938	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12644947	0.97[ASN][1000 genomes]
rs13103374	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13104555	0.81[AMR][1000 genomes]
rs13112959	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1436521	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1436527	0.93[ASN][1000 genomes]
rs1469869	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2118044	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2589514	0.91[ASN][1000 genomes]
rs3775181	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3775183	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3775187	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4133139	0.99[ASN][1000 genomes]
rs4364253	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4482754	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4487330	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4501213	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6531896	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6810413	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6822410	0.83[AMR][1000 genomes]
rs6840318	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7692676	0.91[ASN][1000 genomes]
rs9884770	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9995879	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9996208	0.99[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	nsv1009622	chr4:86893536-87119153	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1003585	chr4:86957967-87250436	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv594761	chr4:86976413-87018488	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv2754254	chr4:86979147-87108510	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv879521	chr4:86979927-87165758	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87004000-87028400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr4:87004200-87006400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr4:87005000-87007600	Weak transcription	Small Intestine	intestine
4	chr4:87005000-87011000	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr4:87005000-87050400	Weak transcription	Brain Angular Gyrus	brain
6	chr4:87005200-87007200	Weak transcription	Brain Hippocampus Middle	brain
7	chr4:87005400-87010200	Weak transcription	Brain Germinal Matrix	brain
8	chr4:87005400-87010400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr4:87005400-87011000	Weak transcription	Brain Anterior Caudate	brain
10	chr4:87005400-87011000	Weak transcription	Pancreas	Pancrea
11	chr4:87005400-87011200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr4:87005400-87028200	Weak transcription	Ovary	ovary
13	chr4:87005400-87028400	Weak transcription	Fetal Stomach	stomach
14	chr4:87005600-87007000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr4:87005600-87010800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr4:87005600-87023000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr4:87005600-87026200	Weak transcription	Brain Cingulate Gyrus	brain
18	chr4:87005600-87031200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr4:87005600-87035200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:87005800-87006600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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