Variant report

Variant	rs371454
Chromosome Location	chr9:6078614-6078615
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:5878375..5880151-chr9:6078401..6080050,2	K562	blood:
2	chr9:6067676..6070179-chr9:6077963..6079813,2	MCF-7	breast:
3	chr9:6068346..6070215-chr9:6077181..6078766,2	K562	blood:
4	chr9:6074105..6076880-chr9:6078281..6080454,2	K562	blood:

Extended variants
information (count: 95 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10124484	1.00[CHB][hapmap]
rs10739084	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10975412	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10975413	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10975416	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12337790	1.00[CHB][hapmap]
rs12339889	1.00[CHB][hapmap]
rs12341021	1.00[CHB][hapmap]
rs1330124	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1332291	0.84[EUR][1000 genomes]
rs1332292	0.91[EUR][1000 genomes]
rs1537285	0.91[EUR][1000 genomes]
rs1556470	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1591044	0.91[EUR][1000 genomes]
rs168168	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1755531	0.91[EUR][1000 genomes]
rs189348	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1970089	0.91[EUR][1000 genomes]
rs1993912	1.00[CHB][hapmap]
rs2150969	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs340887	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs340893	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs340894	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs340896	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs340901	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs340902	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs340903	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs340904	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs340905	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs340906	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs340918	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs340919	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs340921	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs340922	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs340923	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs340924	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs340925	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs340926	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs340933	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs340934	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs340935	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs343475	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs343476	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs343479	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs343489	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs343490	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs343491	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs343495	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs343496	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs369996	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs371165	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs372560	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs374672	0.91[EUR][1000 genomes]
rs375560	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs376690	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs378952	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs380568	0.87[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs380888	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs390158	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs393556	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs394879	0.82[EUR][1000 genomes]
rs397505	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs397916	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs398561	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs399834	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs401731	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs401834	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs413382	0.81[EUR][1000 genomes]
rs420445	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs425489	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs437389	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs441616	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs442851	0.91[EUR][1000 genomes]
rs443175	0.91[EUR][1000 genomes]
rs451974	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs454664	1.00[ASN][1000 genomes]
rs503384	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs503507	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs531759	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62558390	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs639247	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs694796	0.91[EUR][1000 genomes]
rs695013	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7850455	0.81[EUR][1000 genomes]
rs7859471	1.00[CHB][hapmap]
rs821164	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9407312	0.91[EUR][1000 genomes]
rs9408638	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs974936	0.88[AMR][1000 genomes];0.93[EUR][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	nsv948847	chr9:5712626-6417677	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv1015450	chr9:5915640-6114652	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv613205	chr9:6032924-6332901	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv916394	chr9:6055497-6322471	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs371454	C9orf68	cis	cerebellum	SCAN
rs371454	C9orf70	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6068800-6079400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:6069600-6079600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr9:6073400-6079200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr9:6073800-6079800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr9:6074600-6079800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr9:6075600-6079800	Weak transcription	Stomach Mucosa	stomach
7	chr9:6077200-6079400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr9:6077400-6079800	Weak transcription	Osteobl	bone
9	chr9:6077400-6080000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr9:6077600-6079600	Weak transcription	HMEC	breast
11	chr9:6077600-6079600	Weak transcription	NHEK	skin
12	chr9:6077800-6079600	Weak transcription	Psoas Muscle	Psoas
13	chr9:6078000-6079400	Enhancers	K562	blood
14	chr9:6078200-6079000	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr9:6078200-6079200	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr9:6078200-6079800	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr9:6078200-6079800	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr9:6078200-6080600	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr9:6078400-6078800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr9:6078400-6078800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr9:6078400-6078800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr9:6078400-6079200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr9:6078400-6080000	Enhancers	Fetal Heart	heart
24	chr9:6078600-6078800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr9:6078600-6079000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr9:6078600-6079000	Weak transcription	Hela-S3	cervix

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