Variant report

Variant	rs12002475
Chromosome Location	chr9:118275670-118275671
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]
rs12000608	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12003493	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1335142	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2188050	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2188068	1.00[AFR][1000 genomes]
rs62575261	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs62575263	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs62575306	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs62575307	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs62575309	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs62575310	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs62576499	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62576500	0.81[ASN][1000 genomes]
rs62576501	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62576502	0.85[ASN][1000 genomes]
rs62576506	0.80[AMR][1000 genomes]
rs62576528	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62576529	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62576530	0.93[EUR][1000 genomes]
rs62576532	0.93[EUR][1000 genomes]
rs62576533	0.91[EUR][1000 genomes]
rs62576534	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62576535	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62576536	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62576537	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62576538	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62576539	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62576662	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62576663	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62576664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62576666	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62576667	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62576696	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs62576698	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs62576702	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72755374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72757379	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs72759322	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72763123	1.00[AFR][1000 genomes];0.82[AMR][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	nsv615251	chr9:117975864-118514444	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv948346	chr9:118107565-118718197	Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1042957	chr9:118153824-118313540	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1046948	chr9:118185587-118926891	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv916622	chr9:118206309-118952390	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv540207	chr9:118206311-118920304	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv491661	chr9:118206312-118802177	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv893770	chr9:118213502-118299750	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv893771	chr9:118244107-118332688	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv615252	chr9:118253001-118314667	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv1043001	chr9:118253881-118333900	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12002475	RP11-445L6.3	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:118273400-118276000	Enhancers	ES-I3 Cell Line	embryonic stem cell
2	chr9:118275000-118276600	Enhancers	H9 Cell Line	embryonic stem cell
3	chr9:118275000-118276600	Enhancers	Brain Substantia Nigra	brain
4	chr9:118275000-118277000	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr9:118275000-118277200	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr9:118275000-118277200	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr9:118275000-118277200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr9:118275000-118277400	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr9:118275200-118276000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr9:118275200-118277000	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr9:118275200-118277200	Enhancers	H1 Cell Line	embryonic stem cell
12	chr9:118275200-118277200	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr9:118275400-118279000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr9:118275600-118275800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr9:118275600-118276400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr9:118275600-118280000	Weak transcription	Fetal Lung	lung

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