Variant report

Variant	rs9468217
Chromosome Location	chr6:27726467-27726468
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:27670250..27673191-chr6:27723819..27726632,2	K562	blood:

Extended variants
information (count: 83 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10214440	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10484401	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1139226	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13211701	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13215072	0.86[EUR][1000 genomes]
rs169262	0.89[ASN][1000 genomes]
rs1985099	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs200468	0.92[ASN][1000 genomes]
rs200474	0.83[ASN][1000 genomes]
rs200475	0.85[ASN][1000 genomes]
rs200476	0.88[ASN][1000 genomes]
rs2056925	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2092075	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2179094	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2179095	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2394000	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2394002	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2893929	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2893930	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2893931	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34752872	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35069907	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35957409	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4140646	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4711163	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4713118	0.87[EUR][1000 genomes]
rs4713121	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6901520	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6902689	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6914924	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6922574	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6930992	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs742046	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs742047	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs760587	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7756968	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7759217	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7760523	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7772027	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7773070	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7776351	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9283880	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9283881	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9283882	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9283883	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9295740	0.88[ASN][1000 genomes]
rs9295742	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9295743	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9295746	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9348774	0.88[ASN][1000 genomes]
rs9348775	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9357045	0.88[ASN][1000 genomes]
rs9366700	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9366702	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9368528	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9368529	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9368530	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9380010	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9380011	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9380012	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9393847	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9393848	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9461401	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9461405	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9461406	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9468195	0.87[EUR][1000 genomes]
rs9468199	0.81[ASN][1000 genomes]
rs9468200	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9468201	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9468203	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9468204	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9468206	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9468214	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9468219	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9468220	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9468223	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9468229	0.89[EUR][1000 genomes];0.92[ASN][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	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv883510	chr6:27550712-27730064	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv830618	chr6:27593274-27789605	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
4	nsv1031337	chr6:27596676-27734884	Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv601205	chr6:27656255-27730064	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv432858	chr6:27719375-28011652	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	387 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9468217	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs9468217	AL022393.7	cis	Muscle Skeletal	GTEx
rs9468217	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs9468217	OR2B8P	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27722600-27728000	Weak transcription	Hela-S3	cervix
2	chr6:27725200-27726800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:27725600-27726600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:27725600-27726600	Enhancers	Fetal Lung	lung
5	chr6:27725600-27728000	Weak transcription	Osteobl	bone
6	chr6:27725600-27729400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr6:27725600-27730200	Weak transcription	NHEK	skin
8	chr6:27725600-27743000	Weak transcription	Right Atrium	heart
9	chr6:27725800-27726600	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr6:27725800-27726600	Bivalent Enhancer	Fetal Muscle Leg	muscle
11	chr6:27725800-27726600	Enhancers	Placenta Amnion	Placenta Amnion
12	chr6:27725800-27726600	Flanking Active TSS	K562	blood
13	chr6:27725800-27727000	Flanking Active TSS	Dnd41	blood
14	chr6:27725800-27728200	Weak transcription	HMEC	breast
15	chr6:27725800-27728400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr6:27725800-27728800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr6:27725800-27728800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr6:27726000-27726800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
19	chr6:27726000-27727000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
20	chr6:27726000-27727800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:27726000-27728600	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr6:27726000-27728800	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr6:27726000-27729200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr6:27726200-27726600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
25	chr6:27726200-27726600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
26	chr6:27726200-27726600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
27	chr6:27726200-27726600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
28	chr6:27726200-27727600	Enhancers	GM12878-XiMat	blood
29	chr6:27726400-27726600	Weak transcription	Fetal Intestine Small	intestine
30	chr6:27726400-27726600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
31	chr6:27726400-27726600	Enhancers	Rectal Mucosa Donor 29	rectum
32	chr6:27726400-27726800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
33	chr6:27726400-27727000	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr6:27726400-27727000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
35	chr6:27726400-27728200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr6:27726400-27728400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr6:27726400-27733000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr6:27726400-27738600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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