Variant report

Variant	rs340935
Chromosome Location	chr9:6080998-6080999
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10739084	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10975412	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10975413	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10975416	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1330124	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1332291	0.81[EUR][1000 genomes]
rs1332292	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1537285	0.88[EUR][1000 genomes]
rs1556470	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1591044	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs168168	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1755531	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs189348	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1970089	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2150969	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs340887	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs340893	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs340894	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs340896	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs340901	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs340902	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs340903	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs340904	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs340905	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs340906	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs340918	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs340919	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs340921	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340922	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340923	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340924	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340925	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340926	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340933	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340934	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs343475	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs343476	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs343479	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs343489	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs343490	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs343491	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs343495	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs343496	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs369996	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs371165	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs371454	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs372560	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs374672	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs375560	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs376690	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs378952	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs380568	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs380888	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs390158	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs393556	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs394879	0.81[AMR][1000 genomes]
rs397505	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs397916	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs398561	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs399834	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs401731	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs401834	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs420445	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs425489	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs437389	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs441616	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs442851	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs443175	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs451974	0.88[EUR][1000 genomes]
rs454664	0.94[ASN][1000 genomes]
rs503384	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs503507	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs531759	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62558390	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs639247	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs694796	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs695013	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs821164	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9407312	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9408638	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs974936	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6079400-6081000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr9:6079400-6081000	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr9:6079400-6081000	Active TSS	Stomach Smooth Muscle	stomach
4	chr9:6079400-6081200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr9:6079400-6081200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr9:6079600-6081000	Active TSS	Fetal Brain Female	brain
7	chr9:6079600-6081000	Active TSS	Fetal Kidney	kidney
8	chr9:6079800-6081000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr9:6079800-6081000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr9:6079800-6081000	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr9:6079800-6081000	Active TSS	Liver	Liver
12	chr9:6079800-6081000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr9:6079800-6081000	Active TSS	Duodenum Mucosa	Duodenum
14	chr9:6079800-6081000	Active TSS	Fetal Intestine Small	intestine
15	chr9:6079800-6081000	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr9:6079800-6081000	Active TSS	Rectal Smooth Muscle	rectum
17	chr9:6079800-6081000	Active TSS	NHDF-Ad	bronchial
18	chr9:6079800-6081000	Active TSS	Osteobl	bone
19	chr9:6080000-6081000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
20	chr9:6080000-6081000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr9:6080000-6081000	Active TSS	Stomach Mucosa	stomach
22	chr9:6080000-6081000	Active TSS	A549	lung
23	chr9:6080200-6081000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
24	chr9:6080600-6081000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr9:6080600-6081000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr9:6080600-6081000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
27	chr9:6080600-6081000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr9:6080600-6081000	Enhancers	K562	blood
29	chr9:6080600-6081000	Flanking Active TSS	NHEK	skin
30	chr9:6080600-6081200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
31	chr9:6080600-6081200	Flanking Active TSS	Hela-S3	cervix
32	chr9:6080600-6081400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr9:6080600-6081600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr9:6080800-6081000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr9:6080800-6081000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr9:6080800-6081000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr9:6080800-6081000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr9:6080800-6081000	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr9:6080800-6081000	Enhancers	Colon Smooth Muscle	Colon
40	chr9:6080800-6081000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
41	chr9:6080800-6081000	Enhancers	HMEC	breast
42	chr9:6080800-6081200	Enhancers	H9 Cell Line	embryonic stem cell
43	chr9:6080800-6081800	Enhancers	H1 Cell Line	embryonic stem cell

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