Variant report

Variant	rs10073609
Chromosome Location	chr5:12330841-12330842
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10035620	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1006242	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1006243	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10065719	0.82[ASN][1000 genomes]
rs10073372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10074595	0.94[ASN][1000 genomes]
rs11133709	0.99[ASN][1000 genomes]
rs1159451	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12651993	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1476767	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2024136	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2024137	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2024138	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2052034	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2108883	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2108884	0.85[ASN][1000 genomes]
rs2191009	0.82[ASN][1000 genomes]
rs2191011	0.83[ASN][1000 genomes]
rs2215203	0.83[ASN][1000 genomes]
rs2215204	0.81[ASN][1000 genomes]
rs2215206	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2215207	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2400143	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2400149	0.96[ASN][1000 genomes]
rs2400151	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2400152	0.82[ASN][1000 genomes]
rs2895619	0.82[ASN][1000 genomes]
rs2907083	0.82[ASN][1000 genomes]
rs4370272	0.82[ASN][1000 genomes]
rs4431335	0.83[ASN][1000 genomes]
rs4701937	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4702865	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6860849	0.86[ASN][1000 genomes]
rs6866137	0.82[ASN][1000 genomes]
rs6891532	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7701646	0.94[ASN][1000 genomes]
rs9312797	0.81[ASN][1000 genomes]
rs9312800	0.83[ASN][1000 genomes]
rs9632429	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025096	chr5:12049731-12778382	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv537660	chr5:12049731-12778382	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv880704	chr5:12132401-12338203	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv880364	chr5:12153033-12330841	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1030580	chr5:12254774-12364629	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1015676	chr5:12276531-12540904	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv427711	chr5:12285375-12747819	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv1026529	chr5:12285675-12387812	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv1017000	chr5:12285675-12451819	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv537664	chr5:12285675-12451819	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv917255	chr5:12310838-12929427	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10073609	TRIO	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:12330000-12331600	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr5:12330000-12333400	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr5:12330000-12333400	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr5:12330000-12333800	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr5:12330200-12331400	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr5:12330200-12331800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr5:12330400-12331000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr5:12330400-12331400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr5:12330400-12331600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr5:12330400-12333200	Enhancers	H1 Cell Line	embryonic stem cell
11	chr5:12330400-12333600	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr5:12330400-12333600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr5:12330400-12334200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr5:12330600-12332000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
15	chr5:12330800-12331400	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr5:12330800-12338000	Weak transcription	H9 Cell Line	embryonic stem cell

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