Variant report

Variant	rs742047
Chromosome Location	chr6:27739380-27739381
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:27734440..27736801-chr6:27737530..27740059,2	MCF-7	breast:
2	chr6:27739073..27741027-chr6:27745777..27747654,2	MCF-7	breast:
3	chr6:27739033..27741746-chr6:27859741..27864779,4	MCF-7	breast:
4	chr6:27738868..27742221-chr6:27743370..27745719,4	MCF-7	breast:
5	chr6:27738620..27740539-chr6:27758419..27760190,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197153	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000196331	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 11 )

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

rs_ID	r²[population]
rs10214440	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10484401	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.90[YRI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1139226	0.86[EUR][1000 genomes]
rs13211701	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13215072	0.86[EUR][1000 genomes]
rs169262	0.91[ASN][1000 genomes]
rs1985099	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs200468	0.92[ASN][1000 genomes]
rs200474	0.85[ASN][1000 genomes]
rs200475	0.88[ASN][1000 genomes]
rs200476	0.90[ASN][1000 genomes]
rs200502	0.90[CEU][hapmap]
rs200956	0.83[CHD][hapmap]
rs200969	0.83[CHD][hapmap]
rs200991	0.83[CHD][hapmap]
rs2056925	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2092075	0.95[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2179094	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2179095	0.95[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2394000	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2394002	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2893929	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2893930	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2893931	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34752872	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35069907	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35957409	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4140646	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4711163	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4713118	0.86[EUR][1000 genomes]
rs4713121	0.95[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs573179	0.83[CHD][hapmap]
rs6901520	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6902689	0.95[CEU][hapmap];0.85[CHB][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6914924	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6922574	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6930992	0.95[CEU][hapmap];0.87[CHB][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs742046	0.95[CEU][hapmap];0.82[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs760587	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7756968	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7759217	0.95[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7760523	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7772027	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7773070	0.95[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7776351	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9283880	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9283881	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9283882	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9283883	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9295740	1.00[CHB][hapmap];0.96[CHD][hapmap];0.86[ASN][1000 genomes]
rs9295742	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9295743	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9295746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9348774	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs9348775	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9357045	0.86[ASN][1000 genomes]
rs9366700	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9366702	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9368528	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9368529	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9368530	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9380010	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9380011	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9380012	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9393847	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9393848	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9461401	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9461405	0.95[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9461406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9468195	0.86[EUR][1000 genomes]
rs9468200	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9468201	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9468203	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9468204	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9468206	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9468214	0.90[CEU][hapmap];0.87[CHB][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9468217	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9468219	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9468220	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468223	0.95[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9468229	0.89[EUR][1000 genomes];0.94[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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs742047	BTN3A3	cis	cerebellum	SCAN
rs742047	BTN3A3	cis	parietal	SCAN
rs742047	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs742047	HIST1H2BM	cis	cerebellum	SCAN
rs742047	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs742047	BTN2A1	cis	cerebellum	SCAN
rs742047	ZKSCAN3	cis	parietal	SCAN
rs742047	OR2B8P	cis	Thyroid	GTEx
rs742047	BTN2A1	cis	parietal	SCAN
rs742047	AL022393.7	cis	Muscle Skeletal	GTEx
rs742047	HIST1H3C	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27725600-27743000	Weak transcription	Right Atrium	heart
2	chr6:27730600-27740000	Weak transcription	Spleen	Spleen
3	chr6:27730800-27740000	Weak transcription	Primary T cells from cord blood	blood
4	chr6:27737400-27739600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:27738200-27740200	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
6	chr6:27738600-27739400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr6:27738600-27739800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr6:27738600-27739800	Enhancers	Fetal Intestine Large	intestine
9	chr6:27738600-27741600	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr6:27738600-27742400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:27738800-27739400	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
12	chr6:27738800-27739400	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
13	chr6:27738800-27739400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
14	chr6:27738800-27740000	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
15	chr6:27738800-27740800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
16	chr6:27738800-27741800	Enhancers	Primary hematopoietic stem cells	blood
17	chr6:27739000-27739400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:27739000-27739400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr6:27739000-27739400	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr6:27739000-27739600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr6:27739000-27739800	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr6:27739000-27739800	Enhancers	Colonic Mucosa	Colon
23	chr6:27739000-27739800	Enhancers	Fetal Intestine Small	intestine
24	chr6:27739000-27739800	Active TSS	Rectal Mucosa Donor 29	rectum
25	chr6:27739000-27740000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr6:27739000-27740000	Enhancers	K562	blood
27	chr6:27739000-27742000	Enhancers	Monocytes-CD14+_RO01746	blood
28	chr6:27739000-27742400	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr6:27739000-27742400	Enhancers	Primary B cells from peripheral blood	blood
30	chr6:27739200-27739400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
31	chr6:27739200-27739400	Flanking Bivalent TSS/Enh	H9 Cell Line	embryonic stem cell
32	chr6:27739200-27739400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
33	chr6:27739200-27739400	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr6:27739200-27739600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
35	chr6:27739200-27742200	Enhancers	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links