Variant report

Variant	rs9468223
Chromosome Location	chr6:27740666-27740667
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27740046..27740698-chr6:27763330..27763891,2	MCF-7	breast:
2	chr6:27739695..27740963-chr6:27759065..27761089,16	K562	blood:
3	chr6:27095110..27096779-chr6:27740302..27742676,2	K562	blood:
4	chr6:27740030..27740808-chr6:27759602..27760720,5	MCF-7	breast:
5	chr6:27739073..27741027-chr6:27745777..27747654,2	MCF-7	breast:
6	chr6:27739947..27740882-chr6:27863320..27863903,2	MCF-7	breast:
7	chr6:27739033..27741746-chr6:27859741..27864779,4	MCF-7	breast:
8	chr6:27740321..27742174-chr6:27780434..27782983,2	MCF-7	breast:
9	chr6:27738868..27742221-chr6:27743370..27745719,4	MCF-7	breast:
10	chr6:27113969..27118292-chr6:27739764..27746039,7	K562	blood:
11	chr6:27739903..27740843-chr6:27759520..27760687,12	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000196374	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000182611	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000233224	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10214440	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10484401	0.95[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1139226	0.82[EUR][1000 genomes]
rs13211701	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13215072	0.82[EUR][1000 genomes]
rs169262	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1985099	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs200468	0.89[AFR][1000 genomes];0.82[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];0.92[ASN][1000 genomes]
rs200476	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs200502	0.82[CEU][hapmap]
rs2056925	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2092075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2179094	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2179095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2394000	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2394002	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2893929	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2893930	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2893931	1.00[AFR][1000 genomes];0.93[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	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35957409	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4140646	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4711163	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4713118	0.82[EUR][1000 genomes]
rs4713121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6901520	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6902689	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6914924	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6922574	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6930992	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs742046	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs742047	0.95[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs760587	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7756968	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7759217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7760523	0.87[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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7776351	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9283880	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9283881	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9283882	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9283883	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9295740	0.87[CHB][hapmap];0.82[ASN][1000 genomes]
rs9295742	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9295743	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9295746	0.95[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9348774	0.88[CHB][hapmap];0.82[ASN][1000 genomes]
rs9348775	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9357045	0.82[ASN][1000 genomes]
rs9366700	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9366702	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[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	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[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	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9461405	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9461406	0.95[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];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	0.95[CEU][hapmap];0.88[CHB][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9468214	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9468217	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9468219	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9468220	0.95[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9468229	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[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
rs9468223	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs9468223	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs9468223	AL022393.7	cis	Muscle Skeletal	GTEx
rs9468223	OR2B8P	cis	Thyroid	GTEx

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27725600-27743000	Weak transcription	Right Atrium	heart
2	chr6:27738600-27741600	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr6:27738600-27742400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr6:27738800-27740800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
5	chr6:27738800-27741800	Enhancers	Primary hematopoietic stem cells	blood
6	chr6:27739000-27742000	Enhancers	Monocytes-CD14+_RO01746	blood
7	chr6:27739000-27742400	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr6:27739000-27742400	Enhancers	Primary B cells from peripheral blood	blood
9	chr6:27739200-27742200	Enhancers	GM12878-XiMat	blood
10	chr6:27739400-27740800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:27739400-27741600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
12	chr6:27739800-27740800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr6:27739800-27740800	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr6:27739800-27740800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr6:27739800-27740800	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
16	chr6:27739800-27740800	Flanking Active TSS	Duodenum Mucosa	Duodenum
17	chr6:27739800-27740800	Flanking Active TSS	Fetal Intestine Large	intestine
18	chr6:27739800-27740800	Enhancers	Placenta	Placenta
19	chr6:27739800-27740800	Bivalent Enhancer	Fetal Thymus	thymus
20	chr6:27739800-27741000	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
21	chr6:27739800-27741000	Enhancers	Primary T cells fromperipheralblood	blood
22	chr6:27739800-27741200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
23	chr6:27739800-27742400	Enhancers	Primary B cells from cord blood	blood
24	chr6:27740000-27740800	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr6:27740000-27740800	Enhancers	Fetal Muscle Trunk	muscle
26	chr6:27740000-27740800	Bivalent Enhancer	Fetal Muscle Leg	muscle
27	chr6:27740000-27740800	Flanking Active TSS	Hela-S3	cervix
28	chr6:27740000-27741000	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr6:27740000-27741000	Active TSS	Rectal Smooth Muscle	rectum
30	chr6:27740000-27741200	Flanking Active TSS	HepG2	liver
31	chr6:27740000-27741800	Flanking Active TSS	K562	blood
32	chr6:27740000-27742200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr6:27740000-27742200	Enhancers	Stomach Mucosa	stomach
34	chr6:27740200-27740800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr6:27740200-27740800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr6:27740200-27740800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
37	chr6:27740200-27740800	Enhancers	Placenta Amnion	Placenta Amnion
38	chr6:27740200-27740800	Flanking Active TSS	Dnd41	blood
39	chr6:27740200-27741200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr6:27740200-27741400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr6:27740200-27741800	Enhancers	Primary neutrophils fromperipheralblood	blood
42	chr6:27740200-27745200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr6:27740400-27740800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
44	chr6:27740400-27740800	Enhancers	Fetal Stomach	stomach
45	chr6:27740400-27740800	Enhancers	NHDF-Ad	bronchial
46	chr6:27740400-27740800	Enhancers	NHEK	skin
47	chr6:27740400-27741000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr6:27740400-27741000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
49	chr6:27740400-27741600	Enhancers	Colonic Mucosa	Colon
50	chr6:27740400-27741600	Enhancers	Spleen	Spleen

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