Variant report

Variant	rs9380010
Chromosome Location	chr6:27683572-27683573
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:27677806..27681371-chr6:27682071..27685052,3	K562	blood:
2	chr6:27683083..27685640-chr6:27686917..27688772,2	MCF-7	breast:
3	chr6:27676729..27679149-chr6:27683111..27685492,2	K562	blood:

Extended variants
information (count: 88 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10214440	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10484401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.83[TSI][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1139226	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13211701	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13215072	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1985099	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs200468	0.81[ASN][1000 genomes]
rs200502	0.90[CEU][hapmap]
rs200956	0.83[CHD][hapmap];0.84[LWK][hapmap]
rs200969	0.83[CHD][hapmap];0.84[LWK][hapmap]
rs200991	0.83[CHD][hapmap]
rs2056925	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2092075	0.95[CEU][hapmap];0.87[CHB][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2179094	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2179095	0.95[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2394000	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2394002	0.88[EUR][1000 genomes]
rs2893929	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2893930	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2893931	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34752872	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35069907	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35957409	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4140646	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4711163	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4713118	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4713121	0.95[CEU][hapmap];0.87[CHB][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs573179	0.83[CHD][hapmap];0.84[LWK][hapmap]
rs6901520	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6902689	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6914924	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6922574	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6930992	0.95[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs742046	0.95[CEU][hapmap];0.82[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs742047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs760587	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7756968	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7759217	0.95[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7760523	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7772027	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7773070	0.95[CEU][hapmap];0.87[CHB][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7776351	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9283880	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9283881	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9283882	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9283883	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9295740	0.88[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9295742	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9295743	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9295746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9348774	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9348775	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9357045	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9366700	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9366702	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9368528	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9368529	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9368530	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9380011	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9380012	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9393847	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9393848	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461401	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9461405	0.95[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap];0.82[TSI][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9461406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9468195	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9468199	0.92[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9468200	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468201	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468203	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468204	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468214	0.90[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9468217	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9468219	0.89[EUR][1000 genomes]
rs9468220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9468223	0.95[CEU][hapmap];0.87[CHB][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9468229	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv1023673	chr6:27570731-27688782	Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv437481	chr6:27655096-27683572	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv601204	chr6:27655564-27689502	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	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
9	nsv437482	chr6:27670917-27683572	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	esv3327708	chr6:27683503-27692934	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs9380010	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs9380010	AL022393.7	cis	Muscle Skeletal	GTEx
rs9380010	HIST1H3C	cis	cerebellum	SCAN
rs9380010	BTN2A1	cis	cerebellum	SCAN
rs9380010	BTN3A3	cis	parietal	SCAN
rs9380010	BTN3A3	cis	cerebellum	SCAN
rs9380010	OR2B8P	cis	Thyroid	GTEx
rs9380010	BTN2A1	cis	parietal	SCAN
rs9380010	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs9380010	ZKSCAN3	cis	parietal	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27662400-27684600	Weak transcription	Lung	lung
2	chr6:27662400-27685600	Weak transcription	Esophagus	oesophagus
3	chr6:27662600-27684000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr6:27662800-27684000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr6:27662800-27684800	Weak transcription	Fetal Kidney	kidney
6	chr6:27662800-27688400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:27662800-27688600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr6:27662800-27689000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr6:27663000-27688600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr6:27663200-27683800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:27663200-27688400	Weak transcription	HMEC	breast
12	chr6:27663400-27687800	Weak transcription	NHEK	skin
13	chr6:27664600-27684600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr6:27668200-27684400	Weak transcription	Fetal Muscle Trunk	muscle
15	chr6:27669800-27684400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr6:27671400-27687200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr6:27671600-27688600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr6:27673000-27684800	Weak transcription	Primary hematopoietic stem cells	blood
19	chr6:27673200-27684800	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr6:27673600-27687600	Weak transcription	Fetal Intestine Small	intestine
21	chr6:27674600-27687000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr6:27675200-27685000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr6:27677800-27683600	Weak transcription	Small Intestine	intestine
24	chr6:27678800-27684000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr6:27678800-27689000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr6:27679000-27685000	Weak transcription	Fetal Lung	lung
27	chr6:27679200-27686600	Weak transcription	Fetal Brain Male	brain
28	chr6:27679400-27688400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr6:27681200-27683800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr6:27681200-27685000	Weak transcription	Fetal Thymus	thymus
31	chr6:27681200-27685200	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr6:27681200-27685600	Weak transcription	Primary T cells from cord blood	blood
33	chr6:27681200-27685600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr6:27681200-27686600	Weak transcription	K562	blood
35	chr6:27681200-27687000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr6:27681200-27687200	Weak transcription	HepG2	liver
37	chr6:27681200-27688200	Weak transcription	A549	lung
38	chr6:27681200-27688600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr6:27681200-27688600	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr6:27681200-27688600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr6:27681200-27688800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr6:27681200-27688800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr6:27681400-27684200	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr6:27681400-27684400	Weak transcription	Thymus	Thymus
45	chr6:27681400-27686200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr6:27681600-27692200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr6:27681800-27683800	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr6:27681800-27683800	Weak transcription	Brain Germinal Matrix	brain
49	chr6:27681800-27684600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr6:27681800-27684800	Weak transcription	Primary B cells from peripheral blood	blood

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