Variant report

Variant	rs10815828
Chromosome Location	chr9:8348602-8348603
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10511491	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10732364	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10733545	0.86[JPT][hapmap]
rs10739155	0.83[GIH][hapmap];0.84[TSI][hapmap]
rs10739156	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10739157	0.95[CHB][hapmap]
rs10739158	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10739159	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10739160	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10758956	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10758957	0.88[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10758958	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10758959	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10758963	0.91[CHB][hapmap]
rs10815823	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10815826	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10815827	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10815829	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10815830	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10815832	0.95[CHB][hapmap]
rs10976970	0.87[ASN][1000 genomes]
rs10976987	0.95[CHB][hapmap]
rs10976989	0.92[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap]
rs10977006	0.85[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap]
rs11794527	0.88[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12238805	0.81[ASN][1000 genomes]
rs1392518	0.87[CHB][hapmap]
rs1500320	0.88[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap]
rs1500321	0.82[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs1500322	0.87[CHB][hapmap]
rs1500323	0.87[CHB][hapmap]
rs16927668	0.91[CHB][hapmap]
rs20513	0.92[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap]
rs28891834	0.87[ASN][1000 genomes]
rs3736381	0.95[CHB][hapmap]
rs3765142	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3765143	0.95[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs3780337	0.87[ASN][1000 genomes]
rs3847290	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3902903	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4740935	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4740936	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4740937	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4740939	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4740940	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4740941	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4742483	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4742485	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4742487	0.81[JPT][hapmap]
rs4742490	0.91[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap]
rs6477294	0.81[CHB][hapmap]
rs6477295	0.80[CHB][hapmap]
rs7018576	0.92[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap]
rs7022162	0.83[CHB][hapmap]
rs7032880	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7850069	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7851892	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7853112	0.95[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap];0.87[ASN][1000 genomes]
rs7856860	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7856922	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7857177	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7864500	0.95[CHB][hapmap]
rs7873177	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10815828	RANBP6	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8330200-8364200	Weak transcription	Brain Anterior Caudate	brain
2	chr9:8339600-8364400	Weak transcription	Brain Germinal Matrix	brain
3	chr9:8339600-8397600	Weak transcription	Fetal Muscle Leg	muscle
4	chr9:8340200-8366400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr9:8340400-8364600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr9:8340800-8364400	Weak transcription	Fetal Brain Female	brain
7	chr9:8341800-8372600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr9:8344400-8349200	Weak transcription	Fetal Lung	lung
9	chr9:8348000-8350400	Enhancers	Brain Cingulate Gyrus	brain
10	chr9:8348000-8350400	Enhancers	Brain Hippocampus Middle	brain
11	chr9:8348400-8350400	Enhancers	Fetal Heart	heart
12	chr9:8348600-8348800	Enhancers	Brain Angular Gyrus	brain
13	chr9:8348600-8348800	Enhancers	Ovary	ovary
14	chr9:8348600-8349000	Flanking Active TSS	Brain Substantia Nigra	brain
15	chr9:8348600-8350000	Enhancers	Brain Inferior Temporal Lobe	brain

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