Variant report

Variant	rs9662288
Chromosome Location	chr1:77389416-77389417
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11162233	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1252485	0.90[ASN][1000 genomes]
rs1252579	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1252586	0.83[ASN][1000 genomes]
rs12722889	0.88[EUR][1000 genomes]
rs1273142	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12731790	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs12734069	0.88[CEU][hapmap];0.94[CHB][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12734254	0.88[CEU][hapmap];0.94[CHB][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12734482	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1357331	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs1403244	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1522621	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1522622	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs1533849	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1533850	0.85[ASN][1000 genomes]
rs1546319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1718920	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17368584	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1766286	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2103039	0.85[ASN][1000 genomes]
rs2350526	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28858794	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34654786	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34701857	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4562675	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4949752	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4949753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4949754	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6703662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71658713	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71658714	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7419029	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7535901	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9659921	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9660283	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9661727	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9725074	0.83[ASN][1000 genomes]
rs9727199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9793293	0.81[EUR][1000 genomes];0.91[ASN][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	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	nsv1005649	chr1:77141039-77398747	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv999350	chr1:77375536-77430222	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv871501	chr1:77382835-77444267	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	n/a	n/a	inside rSNPs	diseases
6	nsv1005548	chr1:77388792-77430739	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77374600-77396200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr1:77385200-77390400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:77385200-77396600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:77385800-77396000	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr1:77386800-77393600	Weak transcription	Cortex derived primary cultured neurospheres	brain

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