Variant report

Variant	rs1865340
Chromosome Location	chr9:8719549-8719550
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10122099	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10815926	0.88[CEU][hapmap];0.89[CHB][hapmap];0.95[EUR][1000 genomes]
rs12375677	0.85[JPT][hapmap];0.81[EUR][1000 genomes]
rs1368979	0.85[JPT][hapmap];0.80[EUR][1000 genomes]
rs1434260	0.85[JPT][hapmap];0.80[EUR][1000 genomes]
rs1473822	0.80[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1821429	0.85[JPT][hapmap];0.81[EUR][1000 genomes]
rs1877447	0.89[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2053126	0.95[EUR][1000 genomes]
rs4614053	0.84[EUR][1000 genomes]
rs4740959	0.85[EUR][1000 genomes]
rs7866681	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7866922	0.92[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs906635	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs906636	0.92[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs980404	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]

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	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
2	nsv892235	chr9:8700396-8865925	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv6474	chr9:8706602-8751414	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1025800	chr9:8712487-9030627	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv539980	chr9:8712487-9030627	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1865340	TAB3	trans	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8704400-8731800	Weak transcription	Fetal Lung	lung
2	chr9:8710600-8733600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr9:8715400-8723000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:8715600-8720200	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr9:8716200-8720200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr9:8716200-8732600	Weak transcription	Fetal Brain Female	brain
7	chr9:8717000-8721000	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr9:8717200-8721000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr9:8717400-8719600	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr9:8717400-8719800	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr9:8717400-8720200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr9:8717800-8720000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr9:8717800-8723400	Enhancers	Primary hematopoietic stem cells	blood
14	chr9:8718000-8721400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr9:8718000-8724600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr9:8718400-8733600	Weak transcription	Psoas Muscle	Psoas
17	chr9:8718600-8720200	Enhancers	Dnd41	blood
18	chr9:8718600-8721200	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr9:8718800-8721000	Enhancers	Placenta Amnion	Placenta Amnion
20	chr9:8718800-8724400	Weak transcription	Ovary	ovary
21	chr9:8718800-8730800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr9:8718800-8732800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr9:8719000-8720000	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr9:8719000-8720000	Weak transcription	HUVEC	blood vessel
25	chr9:8719000-8720200	Weak transcription	Brain Substantia Nigra	brain
26	chr9:8719000-8720600	Enhancers	Brain Anterior Caudate	brain
27	chr9:8719000-8720800	Weak transcription	Aorta	Aorta
28	chr9:8719000-8723800	Weak transcription	Brain Angular Gyrus	brain
29	chr9:8719000-8725600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr9:8719000-8730800	Weak transcription	Brain Cingulate Gyrus	brain
31	chr9:8719000-8733200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr9:8719000-8733200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr9:8719200-8719600	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr9:8719200-8720200	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr9:8719200-8722600	Weak transcription	Brain Hippocampus Middle	brain
36	chr9:8719400-8720200	Weak transcription	Fetal Stomach	stomach
37	chr9:8719400-8725600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr9:8719400-8727000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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