Variant report

Variant	rs2179094
Chromosome Location	chr6:27741825-27741826
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:27095110..27096779-chr6:27740302..27742676,2	K562	blood:
2	chr6:27114542..27117845-chr6:27741589..27745932,6	K562	blood:
3	chr6:27740321..27742174-chr6:27780434..27782983,2	MCF-7	breast:
4	chr6:27653465..27656102-chr6:27740718..27743462,2	K562	blood:
5	chr6:27738868..27742221-chr6:27743370..27745719,4	MCF-7	breast:
6	chr6:27113969..27118292-chr6:27739764..27746039,7	K562	blood:

Variant related genes	Relation type
ENSG00000182611	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000196374	Chromatin interaction
ENSG00000265565	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10214440	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10484401	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1139226	0.82[EUR][1000 genomes]
rs13211701	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13215072	0.81[EUR][1000 genomes]
rs169262	0.93[ASN][1000 genomes]
rs1985099	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs200468	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs200474	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs200475	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs200476	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2056925	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2092075	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2179095	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2394000	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2394002	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2893929	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2893930	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2893931	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34752872	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35069907	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35957409	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4140646	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4711163	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4713118	0.82[EUR][1000 genomes]
rs4713121	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6901520	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6902689	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6914924	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6922574	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6930992	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs742046	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs742047	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs760587	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7756968	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7759217	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7760523	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7772027	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7773070	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7776351	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9283880	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9283881	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9283882	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9283883	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9295740	0.82[ASN][1000 genomes]
rs9295742	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9295743	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9295746	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9348774	0.82[ASN][1000 genomes]
rs9348775	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9357045	0.82[ASN][1000 genomes]
rs9366700	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9366702	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9368528	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9368529	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9368530	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9380010	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9380011	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9380012	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9393847	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9393848	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9461401	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9461405	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9461406	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9468195	0.82[EUR][1000 genomes]
rs9468200	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9468201	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9468203	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9468204	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9468206	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9468214	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9468217	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9468219	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9468220	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9468223	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468229	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	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	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
3	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
4	nsv1017440	chr6:27734824-27864277	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	370 gene(s)	inside rSNPs	diseases
5	nsv1022173	chr6:27734824-27959408	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2179094	AL022393.7	cis	Muscle Skeletal	GTEx
rs2179094	OR2B8P	cis	Thyroid	GTEx
rs2179094	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs2179094	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27725600-27743000	Weak transcription	Right Atrium	heart
2	chr6:27738600-27742400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr6:27739000-27742000	Enhancers	Monocytes-CD14+_RO01746	blood
4	chr6:27739000-27742400	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr6:27739000-27742400	Enhancers	Primary B cells from peripheral blood	blood
6	chr6:27739200-27742200	Enhancers	GM12878-XiMat	blood
7	chr6:27739800-27742400	Enhancers	Primary B cells from cord blood	blood
8	chr6:27740000-27742200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr6:27740000-27742200	Enhancers	Stomach Mucosa	stomach
10	chr6:27740200-27745200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:27740400-27742200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr6:27740400-27742600	Enhancers	Fetal Intestine Small	intestine
13	chr6:27740400-27745200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr6:27740800-27742200	Enhancers	Duodenum Mucosa	Duodenum
15	chr6:27740800-27742600	Enhancers	Fetal Intestine Large	intestine
16	chr6:27740800-27743200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr6:27741000-27743400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr6:27741200-27743600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:27741200-27744600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr6:27741400-27744400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr6:27741600-27742000	Active TSS	Rectal Mucosa Donor 29	rectum
22	chr6:27741600-27742600	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr6:27741800-27742200	Enhancers	HepG2	liver
24	chr6:27741800-27743200	Weak transcription	Primary hematopoietic stem cells	blood
25	chr6:27741800-27744600	Weak transcription	A549	lung
26	chr6:27741800-27744600	Enhancers	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links