Variant report

Variant	rs6477299
Chromosome Location	chr9:8373491-8373492
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10739157	0.90[JPT][hapmap]
rs10758961	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10758963	0.83[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap]
rs10815832	0.83[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap]
rs10976987	0.82[JPT][hapmap]
rs10976989	0.86[CHB][hapmap]
rs10977014	0.83[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1156294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12554953	0.81[JPT][hapmap]
rs1392518	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs1392519	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1500320	0.91[CHB][hapmap]
rs1500322	0.92[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap]
rs1500323	0.92[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap]
rs16927668	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs20513	0.91[CHB][hapmap]
rs2381741	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3736381	0.80[JPT][hapmap]
rs4742488	1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4742490	0.82[CHB][hapmap]
rs6477294	0.95[CHB][hapmap]
rs6477295	0.94[CHB][hapmap]
rs7018576	0.91[CHB][hapmap]
rs7022162	0.91[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap]
rs7038767	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.83[MEX][hapmap];0.95[MKK][hapmap];0.80[TSI][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7864500	0.82[CHB][hapmap];0.81[JPT][hapmap]

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	nsv892225	chr9:8345072-8379313	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
4	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

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8339600-8397600	Weak transcription	Fetal Muscle Leg	muscle
2	chr9:8357200-8374200	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr9:8357600-8381800	Weak transcription	Aorta	Aorta
4	chr9:8361400-8401600	Weak transcription	Fetal Muscle Trunk	muscle
5	chr9:8364600-8382200	Weak transcription	Ovary	ovary
6	chr9:8364800-8376000	Weak transcription	Fetal Brain Male	brain
7	chr9:8364800-8377200	Weak transcription	Fetal Brain Female	brain
8	chr9:8364800-8401600	Weak transcription	Brain Germinal Matrix	brain
9	chr9:8365000-8395400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr9:8365200-8386800	Weak transcription	Brain Anterior Caudate	brain
11	chr9:8365600-8376600	Weak transcription	Brain Substantia Nigra	brain
12	chr9:8365600-8386200	Weak transcription	Brain Angular Gyrus	brain
13	chr9:8365600-8386200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr9:8365800-8375800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr9:8366800-8383000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr9:8367200-8394600	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr9:8367200-8399800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr9:8367600-8376200	Weak transcription	Brain Hippocampus Middle	brain
19	chr9:8371000-8376400	Weak transcription	Primary hematopoietic stem cells	blood
20	chr9:8372000-8374000	Weak transcription	Fetal Lung	lung
21	chr9:8372000-8377800	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr9:8372200-8373600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr9:8372400-8373600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr9:8372600-8373600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr9:8372600-8373600	Enhancers	Placenta Amnion	Placenta Amnion
26	chr9:8372800-8377400	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr9:8373000-8376800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr9:8373000-8402200	Weak transcription	Fetal Kidney	kidney
29	chr9:8373200-8374000	Enhancers	Fetal Heart	heart

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