Variant report

Variant	rs12005477
Chromosome Location	chr9:116412068-116412069
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	chr9:116410997-116412101	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:116410830..116412902-chr9:116418886..116421304,2	MCF-7	breast:
2	chr9:116409796..116412169-chr9:116418517..116420512,2	MCF-7	breast:
3	chr9:116385537..116387562-chr9:116409870..116412944,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000227482	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10981864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12115627	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12115685	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12115728	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12115730	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12553649	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs514603	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs680359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[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	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv893748	chr9:116308709-116421786	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv430093	chr9:116330446-117325446	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
4	nsv893749	chr9:116378759-116439749	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116407000-116413600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr9:116407800-116412600	Weak transcription	Fetal Kidney	kidney
3	chr9:116408200-116412600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:116409000-116412400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr9:116409400-116412400	Enhancers	HepG2	liver
6	chr9:116410200-116412600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
7	chr9:116410200-116412800	Enhancers	Placenta	Placenta
8	chr9:116410200-116413400	Enhancers	Fetal Heart	heart
9	chr9:116410200-116413400	Enhancers	NHDF-Ad	bronchial
10	chr9:116410400-116412200	Enhancers	Brain Angular Gyrus	brain
11	chr9:116410400-116412200	Enhancers	Brain Anterior Caudate	brain
12	chr9:116410400-116412200	Enhancers	Brain Hippocampus Middle	brain
13	chr9:116410400-116412200	Enhancers	Brain Substantia Nigra	brain
14	chr9:116410400-116412200	Enhancers	Spleen	Spleen
15	chr9:116410400-116412400	Enhancers	Brain Cingulate Gyrus	brain
16	chr9:116410400-116412800	Enhancers	Colon Smooth Muscle	Colon
17	chr9:116410400-116413600	Enhancers	Fetal Muscle Leg	muscle
18	chr9:116410400-116413800	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr9:116410400-116415600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr9:116410600-116412400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr9:116410600-116413400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr9:116410600-116413400	Enhancers	NHLF	lung
23	chr9:116410600-116413800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr9:116410800-116414800	Weak transcription	Fetal Intestine Large	intestine
25	chr9:116411000-116413600	Enhancers	Fetal Stomach	stomach
26	chr9:116411000-116415000	Weak transcription	Fetal Intestine Small	intestine
27	chr9:116411000-116416200	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr9:116411200-116413400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr9:116411200-116413400	Enhancers	Ovary	ovary
30	chr9:116411200-116415400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr9:116411400-116412400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr9:116411400-116413800	Enhancers	HUVEC	blood vessel
33	chr9:116411400-116415400	Enhancers	Osteobl	bone
34	chr9:116411400-116416600	Weak transcription	Adipose Nuclei	Adipose
35	chr9:116411600-116412400	Enhancers	Fetal Muscle Trunk	muscle
36	chr9:116411600-116413400	Enhancers	NH-A	brain
37	chr9:116411600-116420000	Weak transcription	Fetal Brain Female	brain
38	chr9:116411800-116412200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr9:116411800-116412600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr9:116411800-116412600	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr9:116411800-116417800	Enhancers	Liver	Liver
42	chr9:116412000-116412600	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr9:116412000-116412800	Weak transcription	Left Ventricle	heart
44	chr9:116412000-116414000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr9:116412000-116414200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr9:116412000-116414200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr9:116412000-116414200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr9:116412000-116414800	Weak transcription	Stomach Smooth Muscle	stomach
49	chr9:116412000-116415000	Weak transcription	Right Atrium	heart
50	chr9:116412000-116415000	Weak transcription	Right Ventricle	heart

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