Variant report

Variant	rs12340424
Chromosome Location	chr9:8468567-8468568
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10121697	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10122691	0.84[ASN][1000 genomes]
rs10758975	0.89[CEU][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes]
rs10815880	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];0.80[JPT][hapmap];0.89[TSI][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10815881	0.94[CEU][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10977124	0.83[EUR][1000 genomes]
rs12349857	0.94[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1359119	0.94[CEU][hapmap];0.90[CHB][hapmap];0.96[GIH][hapmap];0.81[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.96[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1407972	0.89[CEU][hapmap];0.96[GIH][hapmap];0.82[MEX][hapmap];0.84[EUR][1000 genomes]
rs2281747	0.81[MEX][hapmap]
rs2296099	0.89[CEU][hapmap];0.90[CHB][hapmap];0.96[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2296100	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7024486	0.83[MEX][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7028516	0.94[CEU][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7028797	0.94[CEU][hapmap];0.84[CHB][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7044441	0.84[ASN][1000 genomes]
rs7862199	0.81[MEX][hapmap];0.86[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv8414	chr9:7827373-8511613	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1031472	chr9:8250901-8712547	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1022796	chr9:8360729-9110046	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv892226	chr9:8435525-8522326	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv613289	chr9:8456020-8473169	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8418200-8476000	Weak transcription	Fetal Brain Male	brain
2	chr9:8419200-8491000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr9:8420600-8557600	Weak transcription	Aorta	Aorta
4	chr9:8424200-8485000	Weak transcription	Fetal Kidney	kidney
5	chr9:8434200-8485200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr9:8442200-8522200	Weak transcription	Liver	Liver
7	chr9:8448000-8494800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr9:8448400-8472800	Weak transcription	Fetal Stomach	stomach
9	chr9:8451400-8492000	Weak transcription	Psoas Muscle	Psoas
10	chr9:8452400-8475800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr9:8453800-8476200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr9:8458200-8472000	Weak transcription	Fetal Heart	heart
13	chr9:8458800-8471000	Weak transcription	Brain Anterior Caudate	brain
14	chr9:8459000-8476000	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr9:8460200-8473200	Weak transcription	Brain Angular Gyrus	brain
16	chr9:8460400-8475600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr9:8460600-8476000	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr9:8462400-8472800	Weak transcription	Dnd41	blood
19	chr9:8462800-8472400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr9:8464600-8494200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr9:8465400-8475800	Weak transcription	Fetal Muscle Leg	muscle
22	chr9:8465600-8469000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr9:8465600-8470600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr9:8465600-8470600	Weak transcription	Fetal Brain Female	brain
25	chr9:8465600-8470600	Weak transcription	Fetal Muscle Trunk	muscle
26	chr9:8465600-8482600	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr9:8465800-8470000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr9:8465800-8470600	Weak transcription	Brain Germinal Matrix	brain
29	chr9:8465800-8484000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr9:8466000-8469800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr9:8467800-8470800	Strong transcription	Fetal Lung	lung
32	chr9:8468000-8468600	Enhancers	Brain Hippocampus Middle	brain
33	chr9:8468200-8468600	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr9:8468200-8468600	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr9:8468200-8468600	Enhancers	Ovary	ovary
36	chr9:8468400-8468800	Enhancers	Brain Substantia Nigra	brain
37	chr9:8468400-8471200	Strong transcription	Primary hematopoietic stem cells	blood
38	chr9:8468400-8472200	Weak transcription	Brain Cingulate Gyrus	brain
39	chr9:8468400-8478000	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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