Variant report

Variant	rs10961004
Chromosome Location	chr9:13282006-13282007
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr9:13281209-13282177	SK-N-SH	brain:	n/a	n/a
2	TCF12	chr9:13281182-13282161	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:13033734..13035793-chr9:13280439..13283221,2	K562	blood:
2	chr9:13278596..13280107-chr9:13281623..13284453,2	MCF-7	breast:
3	chr9:13281407..13283656-chr9:13286644..13288961,2	MCF-7	breast:
4	chr9:13278089..13282078-chr9:14313109..14316114,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234740	TF binding region
MPDZ	TF binding region
ENSG00000107186	Chromatin interaction
ENSG00000147862	Chromatin interaction
ENSG00000234740	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10756466	0.89[ASN][1000 genomes]
rs10960994	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10960995	0.87[ASN][1000 genomes]
rs10960996	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10960997	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10960998	0.87[ASN][1000 genomes]
rs10960999	0.97[ASN][1000 genomes]
rs10961003	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10961005	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10961007	0.94[ASN][1000 genomes]
rs10961009	0.93[ASN][1000 genomes]
rs1330136	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73647125	0.95[ASN][1000 genomes]
rs7847055	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7855845	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9696523	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892578	chr9:12942956-13485035	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv892583	chr9:13166139-13350478	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv892584	chr9:13214871-13350478	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv427838	chr9:13229753-13393890	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:13279800-13284200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:13280200-13282400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr9:13280200-13282400	Weak transcription	NH-A	brain
4	chr9:13280200-13282600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr9:13280200-13282600	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr9:13280200-13282600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr9:13280200-13282600	Weak transcription	NHDF-Ad	bronchial
8	chr9:13280200-13283000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr9:13280200-13283200	Weak transcription	Fetal Lung	lung
10	chr9:13280200-13283400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr9:13280200-13283600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr9:13280200-13284000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr9:13280200-13284000	Enhancers	Colon Smooth Muscle	Colon
14	chr9:13280200-13284000	Weak transcription	Fetal Kidney	kidney
15	chr9:13280200-13284000	Weak transcription	NHLF	lung
16	chr9:13280200-13284400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr9:13280200-13285200	Weak transcription	Ovary	ovary
18	chr9:13280200-13295600	Weak transcription	Aorta	Aorta
19	chr9:13280400-13282600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr9:13281000-13282400	Weak transcription	Fetal Stomach	stomach
21	chr9:13281000-13283800	Enhancers	Osteobl	bone
22	chr9:13281200-13282800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr9:13281200-13283800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr9:13281200-13285400	Enhancers	Fetal Heart	heart
25	chr9:13281400-13282400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr9:13281800-13282200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr9:13281800-13284600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr9:13282000-13282200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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