Variant report

Variant	rs10977006
Chromosome Location	chr9:8368408-8368409
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10511491	0.85[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap];0.81[TSI][hapmap]
rs10732364	0.91[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs10733545	0.83[CHD][hapmap];0.82[JPT][hapmap]
rs10739155	0.84[GIH][hapmap]
rs10739157	0.91[CHB][hapmap]
rs10739158	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs10739159	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap]
rs10739160	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs10758957	0.80[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs10758963	0.95[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap]
rs10815823	0.81[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.87[JPT][hapmap]
rs10815827	0.85[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap]
rs10815828	0.85[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap]
rs10815832	0.95[CHB][hapmap]
rs10976985	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10976987	0.95[CHB][hapmap]
rs10976989	0.92[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs10976993	0.86[ASN][1000 genomes]
rs10977014	0.82[CHB][hapmap]
rs11794527	0.81[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap]
rs12342923	0.80[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1392518	0.91[CHB][hapmap]
rs1392519	0.82[CHB][hapmap]
rs1500320	0.96[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs1500321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1500322	0.91[CHB][hapmap]
rs1500323	0.91[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap]
rs16927668	0.95[CHB][hapmap]
rs20513	0.92[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs2381741	0.82[CHB][hapmap]
rs3736381	0.90[CHB][hapmap]
rs3765142	0.81[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap]
rs3765143	0.91[CHB][hapmap]
rs3847290	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs4740935	0.95[CHB][hapmap]
rs4740936	0.85[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap]
rs4740937	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs4740939	0.85[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap]
rs4740940	0.85[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap]
rs4740941	0.85[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap]
rs4742487	0.87[JPT][hapmap]
rs4742490	0.89[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6477294	0.81[CHB][hapmap]
rs6477295	0.80[CHB][hapmap]
rs7018576	0.92[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs7032880	0.81[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap]
rs7851892	0.85[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap]
rs7853112	0.91[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap]
rs7856922	0.88[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs7857177	0.88[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap]
rs7864500	0.95[CHB][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10977006	RANBP6	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8339600-8397600	Weak transcription	Fetal Muscle Leg	muscle
2	chr9:8341800-8372600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr9:8350200-8372400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr9:8357200-8374200	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr9:8357600-8381800	Weak transcription	Aorta	Aorta
6	chr9:8361400-8401600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr9:8364600-8370400	Weak transcription	Fetal Lung	lung
8	chr9:8364600-8382200	Weak transcription	Ovary	ovary
9	chr9:8364800-8376000	Weak transcription	Fetal Brain Male	brain
10	chr9:8364800-8377200	Weak transcription	Fetal Brain Female	brain
11	chr9:8364800-8401600	Weak transcription	Brain Germinal Matrix	brain
12	chr9:8365000-8395400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr9:8365200-8386800	Weak transcription	Brain Anterior Caudate	brain
14	chr9:8365600-8376600	Weak transcription	Brain Substantia Nigra	brain
15	chr9:8365600-8386200	Weak transcription	Brain Angular Gyrus	brain
16	chr9:8365600-8386200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr9:8365800-8375800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr9:8366800-8370200	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr9:8366800-8373000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr9:8366800-8383000	Weak transcription	Brain Cingulate Gyrus	brain
21	chr9:8367000-8371600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr9:8367200-8394600	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr9:8367200-8399800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr9:8367600-8376200	Weak transcription	Brain Hippocampus Middle	brain

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