Variant report

Variant	rs199720
Chromosome Location	chr1:77526482-77526483
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11162254	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11162255	0.89[ASN][1000 genomes]
rs11162262	0.85[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs11162265	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11162266	0.88[ASN][1000 genomes]
rs12023405	0.95[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12084236	0.85[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs12132230	0.90[ASN][1000 genomes]
rs12731718	0.89[ASN][1000 genomes]
rs175317	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs187956	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs199662	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs199663	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs199665	1.00[ASN][1000 genomes]
rs199666	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs199668	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs199669	0.98[ASN][1000 genomes]
rs199672	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs199673	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs199696	0.95[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs199699	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs199702	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs199704	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs199707	0.95[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs199709	0.98[ASN][1000 genomes]
rs199716	0.98[ASN][1000 genomes]
rs199717	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs199718	0.98[ASN][1000 genomes]
rs199719	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs199721	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs199722	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs199723	1.00[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.85[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs199724	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2003706	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2281305	0.85[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs34036815	0.88[ASN][1000 genomes]
rs35224101	0.91[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

No data

Chromatin state (count:21 , 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	chr1:77517400-77528800	Weak transcription	Aorta	Aorta
4	chr1:77518200-77533400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:77520400-77549800	Weak transcription	Fetal Stomach	stomach
6	chr1:77521400-77528200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:77521400-77528400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:77523400-77526600	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr1:77523600-77526600	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr1:77524000-77528600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr1:77524400-77526600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:77525200-77526600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:77525200-77526600	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr1:77525200-77528800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr1:77525600-77527800	Genic enhancers	Cortex derived primary cultured neurospheres	brain
16	chr1:77526200-77526600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:77526200-77529000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:77526200-77538000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:77526400-77530000	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr1:77526400-77531200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr1:77526400-77533400	Weak transcription	NHEK	skin

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