Variant report

Variant	rs7776351
Chromosome Location	chr6:27726731-27726732
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:27476075..27477627-chr6:27726656..27728768,2	MCF-7	breast:

Extended variants
information (count: 85 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10214440	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10484401	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];0.93[ASN][1000 genomes]
rs1139226	0.84[EUR][1000 genomes]
rs13211701	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13215072	0.84[EUR][1000 genomes]
rs169262	0.91[ASN][1000 genomes]
rs1985099	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs200468	0.97[ASN][1000 genomes]
rs200474	0.88[ASN][1000 genomes]
rs200475	0.90[ASN][1000 genomes]
rs200476	0.92[ASN][1000 genomes]
rs200502	0.86[CEU][hapmap]
rs200994	0.84[CHD][hapmap];0.84[MEX][hapmap]
rs2056925	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2092075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2179094	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2179095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2394000	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2394002	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2893929	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2893930	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2893931	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34752872	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35069907	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35957409	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4140646	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4711163	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4713118	0.84[EUR][1000 genomes]
rs4713121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6901520	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6902689	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6914924	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6922574	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6930992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs742046	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs742047	0.95[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs760587	0.95[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7756968	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7759217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7760523	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7772027	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7773070	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9283880	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9283881	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9283882	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9283883	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9295740	0.87[CHB][hapmap];0.92[CHD][hapmap];0.84[ASN][1000 genomes]
rs9295742	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9295743	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9295746	0.95[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9295747	0.86[TSI][hapmap]
rs9348774	0.87[CHB][hapmap];0.84[ASN][1000 genomes]
rs9348775	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9357045	0.84[ASN][1000 genomes]
rs9366700	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9366702	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9368528	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9368529	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9368530	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9380010	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9380011	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9380012	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9393847	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9393848	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9461401	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9461405	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9461406	0.95[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9468195	0.84[EUR][1000 genomes]
rs9468200	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9468201	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9468203	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9468204	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9468206	0.95[CEU][hapmap];0.87[CHB][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9468214	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9468217	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9468219	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9468220	0.95[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9468223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9468229	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs7776351	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs7776351	RP1-265C24.5	cis	Muscle Skeletal	GTEx
rs7776351	AL022393.7	cis	Muscle Skeletal	GTEx
rs7776351	HIST1H2BM	cis	cerebellum	SCAN
rs7776351	OR2B8P	cis	Thyroid	GTEx
rs7776351	BTN2A1	cis	parietal	SCAN
rs7776351	HIST1H3D	cis	parietal	SCAN
rs7776351	BTN3A3	cis	cerebellum	SCAN
rs7776351	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs7776351	BTN2A2	Cis_chr	lymphoblastoid	RTeQTL
rs7776351	HIST1H3C	cis	cerebellum	SCAN
rs7776351	BTN3A3	cis	parietal	SCAN
rs7776351	ZKSCAN3	cis	parietal	SCAN

Chromatin state (count:33 , 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	chr6:27725600-27728000	Weak transcription	Osteobl	bone
4	chr6:27725600-27729400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:27725600-27730200	Weak transcription	NHEK	skin
6	chr6:27725600-27743000	Weak transcription	Right Atrium	heart
7	chr6:27725800-27727000	Flanking Active TSS	Dnd41	blood
8	chr6:27725800-27728200	Weak transcription	HMEC	breast
9	chr6:27725800-27728400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr6:27725800-27728800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr6:27725800-27728800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr6:27726000-27726800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
13	chr6:27726000-27727000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
14	chr6:27726000-27727800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr6:27726000-27728600	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr6:27726000-27728800	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr6:27726000-27729200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr6:27726200-27727600	Enhancers	GM12878-XiMat	blood
19	chr6:27726400-27726800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
20	chr6:27726400-27727000	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr6:27726400-27727000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
22	chr6:27726400-27728200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:27726400-27728400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr6:27726400-27733000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr6:27726400-27738600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr6:27726600-27726800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:27726600-27726800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
28	chr6:27726600-27727000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
29	chr6:27726600-27727000	Bivalent Enhancer	Fetal Stomach	stomach
30	chr6:27726600-27727200	Enhancers	Fetal Intestine Small	intestine
31	chr6:27726600-27728400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr6:27726600-27729400	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr6:27726600-27729600	Enhancers	K562	blood

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