Variant report

Variant	rs11802080
Chromosome Location	chr1:175828039-175828040
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11801671	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11802096	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11810072	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11810084	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11810955	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16849261	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16849262	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16849285	0.81[JPT][hapmap]
rs16849286	0.81[JPT][hapmap]
rs478276	0.81[JPT][hapmap]
rs58613222	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59422229	0.96[AFR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72711121	0.97[ASN][1000 genomes]
rs7543556	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33328	chr1:175446583-175910001	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv872560	chr1:175648631-175869554	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv522255	chr1:175827683-175849898	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175815800-175830400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:175822600-175829800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:175826600-175831800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:175827200-175830000	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr1:175827400-175830400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr1:175827400-175830400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr1:175827400-175831000	Weak transcription	Brain Germinal Matrix	brain
8	chr1:175827400-175831600	Weak transcription	Brain Angular Gyrus	brain
9	chr1:175827400-175831600	Weak transcription	Brain Hippocampus Middle	brain
10	chr1:175827400-175831600	Weak transcription	Brain Substantia Nigra	brain
11	chr1:175827400-175832800	Weak transcription	Fetal Brain Female	brain
12	chr1:175827600-175832000	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr1:175827800-175831400	Weak transcription	Brain Anterior Caudate	brain
14	chr1:175827800-175831600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr1:175827800-175831600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr1:175827800-175831800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:175827800-175831800	Weak transcription	Fetal Brain Male	brain

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dbSNP/dbVar ID: rs12345 /nsv7879
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