Variant report

Variant	rs9969780
Chromosome Location	chr9:2614294-2614295
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:2613768..2615804-chr9:2618805..2621446,2	K562	blood:
2	chr9:2613986..2615496-chr9:2621852..2624711,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236404	Chromatin interaction
ENSG00000147852	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10738745	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10757592	0.83[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10967182	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12343894	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1378061	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1869589	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs4741745	1.00[ASW][hapmap];0.80[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes]
rs7046384	0.91[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020530	chr9:1870197-2658587	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv530929	chr9:1998911-2925112	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv466078	chr9:2218129-2621030	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv613126	chr9:2218129-2621030	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv529508	chr9:2267812-2684272	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv916750	chr9:2430846-2826706	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS 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	14 gene(s)	inside rSNPs	diseases
7	nsv531564	chr9:2452325-2700375	Flanking Bivalent TSS/Enh Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv1017581	chr9:2494815-3172020	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
9	nsv539934	chr9:2494815-3172020	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
10	nsv1029876	chr9:2526760-2633562	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv892069	chr9:2600836-2631738	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv892070	chr9:2610307-2633921	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9969780	C9orf46	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:2609600-2615200	Weak transcription	Brain Substantia Nigra	brain
2	chr9:2610600-2615800	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr9:2612000-2616600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr9:2612400-2616000	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr9:2612800-2614600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr9:2612800-2616000	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr9:2613200-2616000	Enhancers	H1 Cell Line	embryonic stem cell
8	chr9:2613200-2616000	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr9:2613200-2616000	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr9:2613400-2614400	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr9:2613400-2614600	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr9:2613400-2616000	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr9:2613600-2614400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr9:2613600-2614400	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr9:2613600-2615000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr9:2613600-2615800	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr9:2613600-2616000	Enhancers	Fetal Kidney	kidney
18	chr9:2613800-2614400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr9:2613800-2614400	Enhancers	Psoas Muscle	Psoas
20	chr9:2613800-2615000	Enhancers	Fetal Stomach	stomach
21	chr9:2613800-2615200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
22	chr9:2614000-2614400	Enhancers	Left Ventricle	heart
23	chr9:2614000-2614400	Enhancers	Placenta Amnion	Placenta Amnion
24	chr9:2614000-2614400	Enhancers	Right Atrium	heart
25	chr9:2614000-2614400	Enhancers	Right Ventricle	heart
26	chr9:2614200-2615400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr9:2614200-2615600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr9:2614200-2615600	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr9:2614200-2615600	Weak transcription	Ovary	ovary
30	chr9:2614200-2618800	Weak transcription	Fetal Heart	heart
31	chr9:2614200-2621000	Weak transcription	Pancreas	Pancrea
32	chr9:2614200-2621200	Weak transcription	Lung	lung

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