Variant report

Variant	rs199669
Chromosome Location	chr1:77540661-77540662
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11162254	0.97[ASN][1000 genomes]
rs11162255	0.87[ASN][1000 genomes]
rs11162262	0.85[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.89[ASN][1000 genomes]
rs11162265	0.84[ASN][1000 genomes]
rs11162266	0.90[ASN][1000 genomes]
rs11162267	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11162268	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12023405	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12084236	0.85[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs12132230	0.89[ASN][1000 genomes]
rs12731718	0.87[ASN][1000 genomes]
rs169215	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs187956	0.97[ASN][1000 genomes]
rs199662	0.80[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.98[ASN][1000 genomes]
rs199663	0.98[ASN][1000 genomes]
rs199665	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs199666	0.98[ASN][1000 genomes]
rs199668	0.92[ASN][1000 genomes]
rs199696	0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs199699	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs199702	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs199704	0.97[ASN][1000 genomes]
rs199707	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs199709	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs199716	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs199717	0.97[ASN][1000 genomes]
rs199718	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs199719	0.80[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs199720	0.80[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.83[YRI][hapmap];0.98[ASN][1000 genomes]
rs199721	0.98[ASN][1000 genomes]
rs199722	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.98[ASN][1000 genomes]
rs199723	0.80[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.98[ASN][1000 genomes]
rs199724	0.80[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.98[ASN][1000 genomes]
rs2003706	0.80[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.80[YRI][hapmap];0.97[ASN][1000 genomes]
rs2281305	0.85[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs34036815	0.87[ASN][1000 genomes]
rs35224101	0.90[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	nsv1003826	chr1:76965331-77656929	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv535006	chr1:76965331-77656929	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv830292	chr1:77425571-77584307	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs199669	SLC44A5	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77506000-77558600	Weak transcription	Stomach Smooth Muscle	stomach
2	chr1:77508600-77547600	Weak transcription	Ovary	ovary
3	chr1:77520400-77549800	Weak transcription	Fetal Stomach	stomach
4	chr1:77529200-77549800	Weak transcription	Aorta	Aorta
5	chr1:77533600-77549800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:77534000-77551400	Weak transcription	NHEK	skin
7	chr1:77534000-77558200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:77534200-77559200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:77538600-77542600	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr1:77539200-77540800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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