Variant report

Variant	rs970946
Chromosome Location	chr9:12738690-12738691
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	chr9:12737180..12738894-chr9:12739213..12741322,2	MCF-7	breast:

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10115741	0.88[ASN][1000 genomes]
rs10120165	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10123986	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10124197	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10733246	0.89[ASN][1000 genomes]
rs10738290	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1074789	0.93[YRI][hapmap]
rs1074790	0.94[ASW][hapmap];0.95[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.81[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.87[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10756399	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10756400	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10756401	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10756402	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10756406	0.89[ASW][hapmap];0.96[YRI][hapmap]
rs10809830	0.83[ASN][1000 genomes]
rs10960776	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10960780	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12342045	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1326779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1326780	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1326781	0.89[ASN][1000 genomes]
rs13289304	0.81[AFR][1000 genomes]
rs1409633	0.80[CHD][hapmap]
rs1543587	0.96[YRI][hapmap]
rs1854022	0.83[ASN][1000 genomes]
rs1887177	0.86[CHB][hapmap];0.80[CHD][hapmap]
rs2147249	0.82[ASN][1000 genomes]
rs2181816	0.87[CHB][hapmap];0.81[JPT][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2209271	0.83[AFR][1000 genomes]
rs2209273	0.86[CHB][hapmap]
rs2382362	0.89[ASN][1000 genomes]
rs2382363	0.86[CHB][hapmap];0.90[CHD][hapmap];0.83[ASN][1000 genomes]
rs2382364	0.86[CHB][hapmap];0.90[CHD][hapmap];0.83[ASN][1000 genomes]
rs2382365	0.89[ASN][1000 genomes]
rs2382368	0.82[ASN][1000 genomes]
rs2890965	0.84[AFR][1000 genomes]
rs4741245	0.96[YRI][hapmap]
rs6474728	0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6474729	0.82[ASN][1000 genomes]
rs7019486	0.89[ASW][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap];0.85[LWK][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7019890	0.89[ASN][1000 genomes]
rs7019981	0.89[ASW][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap];0.83[LWK][hapmap];0.83[MEX][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7028587	0.84[AFR][1000 genomes]
rs7034354	0.84[ASN][1000 genomes]
rs7034577	0.83[ASN][1000 genomes]
rs7035500	0.96[YRI][hapmap]
rs7039957	0.92[CHB][hapmap]
rs7044022	0.84[AFR][1000 genomes]
rs7047704	0.89[ASN][1000 genomes]
rs7048117	0.89[ASN][1000 genomes]
rs7850079	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7871257	0.93[CHB][hapmap];0.95[CHD][hapmap];0.88[MEX][hapmap]
rs927868	0.96[YRI][hapmap]
rs927869	0.83[ASW][hapmap];0.84[LWK][hapmap];0.96[YRI][hapmap]
rs970944	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs970945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs970947	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	nsv1030835	chr9:12717405-12840928	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	esv2757318	chr9:12721881-12758881	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv8420	chr9:12725200-12750151	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	esv3693020	chr9:12726962-12748962	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv818690	chr9:12726962-12748962	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv892573	chr9:12730636-12874703	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
16	nsv516527	chr9:12738690-12748486	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs970946	C9orf150	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:12719200-12740400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:12737400-12739200	Enhancers	Fetal Lung	lung
3	chr9:12737400-12739400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr9:12737600-12741000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:12737800-12739400	Enhancers	NHDF-Ad	bronchial
6	chr9:12737800-12741200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr9:12738000-12738800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr9:12738600-12739600	Enhancers	Cortex derived primary cultured neurospheres	brain

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