Variant report

Variant	rs683
Chromosome Location	chr9:12709305-12709306
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:12708111..12711033-chr9:13076014..13078647,2	MCF-7	breast:

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10491742	1.00[CHB][hapmap]
rs10491743	1.00[ASN][1000 genomes]
rs1063380	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.81[MKK][hapmap];0.85[EUR][1000 genomes]
rs1074789	1.00[CHB][hapmap]
rs10756406	1.00[CHB][hapmap]
rs10809826	1.00[CHB][hapmap]
rs10809829	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10809836	1.00[ASN][1000 genomes]
rs10960758	1.00[ASN][1000 genomes]
rs10960761	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10960762	1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs10960765	1.00[ASN][1000 genomes]
rs10960774	1.00[ASN][1000 genomes]
rs10960779	1.00[ASN][1000 genomes]
rs10960781	1.00[ASN][1000 genomes]
rs12379260	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12552462	1.00[ASN][1000 genomes]
rs1326788	1.00[ASN][1000 genomes]
rs1326789	1.00[ASN][1000 genomes]
rs1326790	1.00[ASN][1000 genomes]
rs1326791	1.00[ASN][1000 genomes]
rs1326792	1.00[ASN][1000 genomes]
rs1326798	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13284445	1.00[ASN][1000 genomes]
rs13284453	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13284467	1.00[ASN][1000 genomes]
rs13284898	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13289304	0.83[ASN][1000 genomes]
rs13293905	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13295868	1.00[ASN][1000 genomes]
rs13302551	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1543587	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17346161	1.00[CHB][hapmap]
rs2209269	1.00[ASN][1000 genomes]
rs2209271	1.00[ASN][1000 genomes]
rs2209277	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2209278	0.81[LWK][hapmap]
rs2224863	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2733830	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2733831	1.00[CHB][hapmap]
rs2733832	1.00[CHB][hapmap];0.87[GIH][hapmap];0.82[AMR][1000 genomes]
rs2733833	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2733834	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2733836	1.00[CHB][hapmap]
rs2762458	1.00[CHB][hapmap]
rs2762460	1.00[ASN][1000 genomes]
rs2762461	1.00[CHB][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2762463	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2762464	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35666741	1.00[ASN][1000 genomes]
rs4741245	1.00[CHB][hapmap]
rs7019226	1.00[ASN][1000 genomes]
rs7021368	1.00[ASN][1000 genomes]
rs7023927	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7025678	1.00[ASN][1000 genomes]
rs7025771	1.00[ASN][1000 genomes]
rs7025812	0.87[EUR][1000 genomes]
rs7025842	1.00[ASN][1000 genomes]
rs7025914	1.00[ASN][1000 genomes]
rs7025953	1.00[ASN][1000 genomes]
rs7028587	1.00[ASN][1000 genomes]
rs7030485	1.00[ASN][1000 genomes]
rs7035500	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7036011	1.00[ASN][1000 genomes]
rs7039325	1.00[ASN][1000 genomes]
rs7466623	1.00[ASN][1000 genomes]
rs910	0.89[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.91[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs927868	1.00[CHB][hapmap]
rs927869	1.00[CHB][hapmap]
rs958073	1.00[CHB][hapmap];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027260	chr9:12196141-12709959	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv540062	chr9:12196141-12709959	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv2759671	chr9:12235048-12784092	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv1034393	chr9:12278703-12798236	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv869288	chr9:12286919-12816766	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv498136	chr9:12387840-12984158	Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv1029415	chr9:12424340-12794623	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv540064	chr9:12424340-12794623	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	esv2422212	chr9:12448789-13127738	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	nsv892572	chr9:12549675-12715816	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv1016570	chr9:12576095-12722387	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	esv2758182	chr9:12621991-12784092	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv466256	chr9:12628213-12712157	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv613612	chr9:12628213-12712157	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv613613	chr9:12641987-12773263	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs683	C9orf150	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:12693000-12710000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr9:12697600-12712200	Weak transcription	Left Ventricle	heart
3	chr9:12708000-12709400	Enhancers	HUVEC	blood vessel
4	chr9:12708200-12709400	Enhancers	Muscle Satellite Cultured Cells	--
5	chr9:12709200-12710000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr9:12709200-12718400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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