Variant report

Variant	rs340904
Chromosome Location	chr9:6106779-6106780
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 94 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10739084	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10975412	0.84[EUR][1000 genomes]
rs10975413	0.87[EUR][1000 genomes]
rs10975416	0.87[EUR][1000 genomes]
rs1330124	0.83[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs1332291	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1332292	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1537285	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1556470	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1591044	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs168168	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1755531	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs189348	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1970089	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2150969	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs340887	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs340893	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs340894	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs340895	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs340896	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340901	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340902	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340903	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340905	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340906	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340918	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs340919	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs340921	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs340922	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs340923	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs340924	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs340925	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs340926	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs340933	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs340934	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs340935	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs343475	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs343476	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs343479	0.87[EUR][1000 genomes]
rs343489	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs343490	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs343491	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs343495	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs343496	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs369996	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs371165	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs371454	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs372560	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs374672	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs375560	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs376690	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs378952	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs380568	0.83[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs380888	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs390158	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs393556	0.84[EUR][1000 genomes]
rs394879	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs397505	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs397916	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs398561	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs399834	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs401731	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs401834	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs413382	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs420445	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs425489	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs437389	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs441616	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs442851	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs443175	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs451974	0.85[EUR][1000 genomes]
rs503384	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs503507	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs531759	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62558390	0.91[EUR][1000 genomes]
rs639247	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs694796	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs695013	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7850455	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs821164	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9407312	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9407324	0.86[AMR][1000 genomes]
rs9408638	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs974936	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948847	chr9:5712626-6417677	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv1015450	chr9:5915640-6114652	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv613205	chr9:6032924-6332901	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv916394	chr9:6055497-6322471	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv2761482	chr9:6084602-6134787	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv892157	chr9:6093790-6322415	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv933124	chr9:6099101-6644738	Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	nsv831496	chr9:6101763-6285088	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs340904	C9orf68	cis	cerebellum	SCAN
rs340904	C9orf70	cis	parietal	SCAN
rs340904	JAK2	cis	cerebellum	SCAN
rs340904	KDM4C	cis	lymphoblastoid	seeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6101600-6107200	Enhancers	HMEC	breast
2	chr9:6103000-6106800	Weak transcription	HUVEC	blood vessel
3	chr9:6103000-6107000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr9:6103000-6108600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr9:6103400-6106800	Weak transcription	NHDF-Ad	bronchial
6	chr9:6103800-6106800	Enhancers	Hela-S3	cervix
7	chr9:6105200-6107200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr9:6105800-6106800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr9:6105800-6107400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr9:6105800-6107400	Enhancers	NHEK	skin
11	chr9:6105800-6107600	Enhancers	Fetal Heart	heart
12	chr9:6106000-6106800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr9:6106000-6107800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr9:6106000-6110200	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr9:6106200-6107000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr9:6106200-6107400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr9:6106200-6110000	Weak transcription	Primary T cells from cord blood	blood
18	chr9:6106200-6110400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr9:6106400-6106800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr9:6106400-6106800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr9:6106600-6106800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr9:6106600-6106800	Enhancers	Brain Hippocampus Middle	brain
23	chr9:6106600-6106800	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr9:6106600-6106800	Enhancers	Stomach Smooth Muscle	stomach
25	chr9:6106600-6106800	Enhancers	GM12878-XiMat	blood
26	chr9:6106600-6107000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr9:6106600-6107200	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr9:6106600-6107200	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr9:6106600-6107200	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr9:6106600-6107400	Enhancers	Fetal Thymus	thymus
31	chr9:6106600-6107400	Enhancers	Stomach Mucosa	stomach
32	chr9:6106600-6107400	Enhancers	Thymus	Thymus
33	chr9:6106600-6107600	Enhancers	Primary hematopoietic stem cells	blood
34	chr9:6106600-6107600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr9:6106600-6107800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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