Variant report

Variant	rs9289488
Chromosome Location	chr3:134710304-134710305
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1020434	1.00[JPT][hapmap]
rs1100567	0.90[ASN][1000 genomes]
rs13353524	0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1350350	0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs16842415	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16842453	0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs16842456	0.95[ASN][1000 genomes]
rs16842468	0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17203924	0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs187585	0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs253878	0.85[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs253880	0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs28223	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs36059	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs36061	0.90[ASN][1000 genomes]
rs36062	0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs36063	0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs36065	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36074	0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs36097	1.00[JPT][hapmap]
rs36102	1.00[JPT][hapmap]
rs36109	1.00[JPT][hapmap]
rs36110	1.00[JPT][hapmap]
rs36111	1.00[JPT][hapmap]
rs36112	1.00[JPT][hapmap]
rs36114	1.00[JPT][hapmap]
rs36115	1.00[JPT][hapmap]
rs36116	1.00[JPT][hapmap]
rs36117	1.00[JPT][hapmap]
rs36121	1.00[JPT][hapmap]
rs36123	1.00[JPT][hapmap]
rs36124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3853726	0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs39698	1.00[JPT][hapmap]
rs39699	1.00[JPT][hapmap]
rs40524	0.85[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4102409	0.90[ASN][1000 genomes]
rs41182	0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs484317	0.85[ASN][1000 genomes]
rs4955533	0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs574719	1.00[JPT][hapmap]
rs6776069	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.86[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6788931	1.00[JPT][hapmap]
rs7650345	1.00[JPT][hapmap]
rs849853	0.85[ASN][1000 genomes]
rs875984	1.00[JPT][hapmap]
rs9832922	1.00[JPT][hapmap]
rs9855772	1.00[JPT][hapmap]
rs9866987	0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[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	nsv1009634	chr3:134543259-134820208	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv536720	chr3:134543259-134820208	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1000277	chr3:134546080-134970837	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv877516	chr3:134689420-134918522	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv877517	chr3:134709951-134805581	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9289488	RAB6B	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134707200-134711000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr3:134708000-134717800	Weak transcription	Psoas Muscle	Psoas
3	chr3:134709400-134711000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr3:134709600-134711800	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr3:134709600-134712000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:134709600-134712800	Enhancers	GM12878-XiMat	blood
7	chr3:134709800-134710800	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr3:134709800-134710800	Enhancers	Brain Germinal Matrix	brain
9	chr3:134709800-134711400	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr3:134709800-134711600	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr3:134710000-134710600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:134710000-134711000	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr3:134710000-134711200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:134710000-134711200	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:134710000-134711400	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr3:134710000-134711400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:134710000-134711400	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr3:134710000-134711600	Enhancers	H1 Cell Line	embryonic stem cell
19	chr3:134710000-134711600	Enhancers	H9 Cell Line	embryonic stem cell
20	chr3:134710000-134711600	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr3:134710000-134711600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:134710000-134712000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr3:134710000-134712400	Enhancers	Brain Anterior Caudate	brain
24	chr3:134710200-134710600	Enhancers	Fetal Brain Male	brain
25	chr3:134710200-134710800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr3:134710200-134711000	Weak transcription	Fetal Brain Female	brain

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