Variant report

Variant	rs6474865
Chromosome Location	chr9:14869861-14869862
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10810272	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10810277	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10810278	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10810283	0.88[CEU][hapmap]
rs10961759	0.86[ASN][1000 genomes]
rs17312753	0.94[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs1889048	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1889049	1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1889051	1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1889052	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1996893	0.81[CEU][hapmap]
rs2065482	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap];0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2065484	0.94[ASN][1000 genomes]
rs2381975	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6474862	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6474863	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6474866	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6474868	0.92[CEU][hapmap];0.94[CHB][hapmap];0.91[ASN][1000 genomes]
rs7019358	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7020282	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7032309	0.80[AMR][1000 genomes]
rs7033932	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7045281	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7048511	0.82[CEU][hapmap]
rs7048783	0.88[CEU][hapmap]
rs73417624	0.95[ASN][1000 genomes]
rs7856810	0.84[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7862066	0.92[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.88[ASN][1000 genomes]
rs7862716	0.94[CHB][hapmap];0.94[CHD][hapmap];0.94[ASN][1000 genomes]
rs7867761	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs7867927	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029491	chr9:14033607-14942373	Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv915804	chr9:14182608-14903050	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv613637	chr9:14524438-15011915	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv831518	chr9:14760638-14953501	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv892617	chr9:14791348-14889834	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv1018416	chr9:14846753-14921247	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv613647	chr9:14852141-15016475	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv3390567	chr9:14852461-14891880	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6474865	LOC93432	trans	cerebellum	SCAN
rs6474865	FREM1	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:14859600-14876600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr9:14860000-14883800	Weak transcription	Fetal Muscle Trunk	muscle
3	chr9:14863800-14870400	Enhancers	Colon Smooth Muscle	Colon
4	chr9:14868600-14870000	Enhancers	Fetal Stomach	stomach
5	chr9:14868800-14870000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr9:14868800-14870400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr9:14869000-14870400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr9:14869000-14870400	Enhancers	Small Intestine	intestine
9	chr9:14869000-14870600	Enhancers	Fetal Lung	lung
10	chr9:14869200-14870000	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr9:14869200-14870000	Flanking Active TSS	Fetal Kidney	kidney
12	chr9:14869200-14870000	Enhancers	Stomach Mucosa	stomach
13	chr9:14869200-14870400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr9:14869200-14876400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr9:14869400-14870400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr9:14869600-14870000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr9:14869600-14870000	Flanking Active TSS	HepG2	liver
18	chr9:14869600-14870600	Enhancers	Duodenum Mucosa	Duodenum
19	chr9:14869800-14870400	Active TSS	Fetal Brain Male	brain

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