Variant report

Variant	rs10977142
Chromosome Location	chr9:8473568-8473569
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10117042	0.81[CEU][hapmap]
rs10217685	0.80[CEU][hapmap]
rs10511496	0.94[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs10815883	1.00[CEU][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10815889	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs10815890	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10815891	0.87[CEU][hapmap]
rs10977131	0.93[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs10977133	0.88[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs10977146	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12341078	0.83[CEU][hapmap]
rs12683581	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12686431	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17650044	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs55663135	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7019398	0.82[CEU][hapmap]
rs7025468	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7858815	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs7862199	0.94[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs7868790	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][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	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

No data

Chromatin state (count:38 , 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	chr9:8451400-8492000	Weak transcription	Psoas Muscle	Psoas
9	chr9:8452400-8475800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr9:8453800-8476200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr9:8459000-8476000	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr9:8460400-8475600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr9:8460600-8476000	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr9:8464600-8494200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr9:8465400-8475800	Weak transcription	Fetal Muscle Leg	muscle
16	chr9:8465600-8482600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr9:8465800-8484000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr9:8468400-8478000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr9:8468600-8474200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr9:8468600-8484000	Weak transcription	Ovary	ovary
21	chr9:8470800-8476200	Weak transcription	Fetal Lung	lung
22	chr9:8471000-8475800	Weak transcription	Fetal Brain Female	brain
23	chr9:8471000-8477600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr9:8471000-8479200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr9:8471200-8474400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr9:8471200-8476000	Weak transcription	Brain Germinal Matrix	brain
27	chr9:8471200-8476000	Weak transcription	Fetal Muscle Trunk	muscle
28	chr9:8471400-8476000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr9:8472000-8474400	Enhancers	Fetal Heart	heart
30	chr9:8472800-8474200	Enhancers	Brain Substantia Nigra	brain
31	chr9:8472800-8475200	Enhancers	Brain Anterior Caudate	brain
32	chr9:8472800-8475200	Enhancers	Dnd41	blood
33	chr9:8473200-8473600	Enhancers	Primary hematopoietic stem cells	blood
34	chr9:8473200-8473600	Weak transcription	Brain Hippocampus Middle	brain
35	chr9:8473200-8474200	Enhancers	Brain Cingulate Gyrus	brain
36	chr9:8473200-8483400	Weak transcription	Fetal Stomach	stomach
37	chr9:8473400-8473600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr9:8473400-8473800	Weak transcription	Brain Angular Gyrus	brain

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