Variant report

Variant	rs9380501
Chromosome Location	chr6:35270579-35270580
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:35267694..35270877-chr6:35436022..35437684,3	K562	blood:
2	chr6:35262159..35262854-chr6:35270058..35270842,2	K562	blood:
3	chr6:35265465..35267988-chr6:35269395..35275247,5	MCF-7	breast:
4	chr6:35269040..35271053-chr6:35276733..35278260,2	K562	blood:
5	chr6:35269302..35271088-chr6:35360750..35362254,2	K562	blood:
6	chr6:35265803..35267846-chr6:35270343..35273998,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198755	Chromatin interaction
ENSG00000023892	Chromatin interaction

Extended variants
information (count: 134 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:132)

rs_ID	r²[population]
rs10080361	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs1013907	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10755687	0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs10807150	0.83[CHB][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10947540	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10947542	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1108709	0.86[ASN][1000 genomes]
rs1194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12173347	0.84[ASN][1000 genomes]
rs12173582	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs12211765	0.87[ASN][1000 genomes]
rs12211943	0.81[ASN][1000 genomes]
rs13214290	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1557567	0.83[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs1557568	0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs1590381	0.86[ASN][1000 genomes]
rs1888822	0.81[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs1888823	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1888824	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1888825	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1894650	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1894651	0.89[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1894652	0.94[ASN][1000 genomes]
rs1894653	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1929847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1929848	0.81[CEU][hapmap];0.85[YRI][hapmap]
rs1929849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1987673	0.83[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs2006184	0.94[ASN][1000 genomes]
rs2018373	0.92[ASN][1000 genomes]
rs2032538	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2071920	0.83[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs2183834	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2267657	0.83[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs2267658	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2267660	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2267661	0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs2267662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2267663	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2267664	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2284195	0.99[ASN][1000 genomes]
rs2395614	0.84[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs34156110	0.82[ASN][1000 genomes]
rs3777742	0.87[ASN][1000 genomes]
rs3777743	0.87[ASN][1000 genomes]
rs3777744	0.82[JPT][hapmap]
rs3798342	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3798343	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs3800382	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3800383	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3800385	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3800386	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3800387	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3800388	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3800392	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3800393	0.85[ASN][1000 genomes]
rs3800396	0.90[ASN][1000 genomes]
rs3800398	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3800399	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3800401	0.81[ASN][1000 genomes]
rs4583983	0.88[ASN][1000 genomes]
rs4711409	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4711411	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4711413	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4711414	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713841	0.90[ASN][1000 genomes]
rs4713845	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4713847	0.85[ASN][1000 genomes]
rs4713848	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4713850	0.81[ASN][1000 genomes]
rs58925593	0.95[ASN][1000 genomes]
rs62403575	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6457812	0.84[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs68164647	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6902523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6906987	0.83[ASN][1000 genomes]
rs6907324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6907364	0.85[ASN][1000 genomes]
rs6907573	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6907795	0.90[ASN][1000 genomes]
rs6913037	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6913475	0.84[ASN][1000 genomes]
rs6913941	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6916364	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6919534	0.81[CEU][hapmap];0.89[YRI][hapmap]
rs6920432	0.83[ASN][1000 genomes]
rs6920747	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6927730	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6928769	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6930562	0.86[ASN][1000 genomes]
rs6933979	0.83[CHB][hapmap]
rs6938946	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6941471	0.88[ASN][1000 genomes]
rs72909061	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7757316	0.83[ASN][1000 genomes]
rs7763946	0.98[ASN][1000 genomes]
rs7769906	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7772212	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7772302	0.82[ASN][1000 genomes]
rs8205	0.88[CEU][hapmap];0.84[CHB][hapmap];0.80[JPT][hapmap];0.90[ASN][1000 genomes]
rs914547	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9296144	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9296150	0.81[ASN][1000 genomes]
rs9348970	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs9366882	0.84[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs9366883	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9366885	0.87[ASN][1000 genomes]
rs9368854	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9368857	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9368859	0.84[ASN][1000 genomes]
rs9368860	0.84[ASN][1000 genomes]
rs9380497	0.81[ASN][1000 genomes]
rs9380498	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9380500	0.83[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs9380502	0.90[ASN][1000 genomes]
rs9394283	0.98[ASN][1000 genomes]
rs9394288	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9394289	0.99[ASN][1000 genomes]
rs9462065	0.84[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs9462072	0.84[ASN][1000 genomes]
rs9469953	0.83[CHB][hapmap]
rs9469964	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9469972	0.83[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs9469975	0.89[ASN][1000 genomes]
rs9469979	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9469982	0.88[CEU][hapmap];0.84[CHB][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9469997	0.81[ASN][1000 genomes]
rs9469998	0.83[ASN][1000 genomes]
rs965272	0.88[CHB][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs968828	0.86[ASN][1000 genomes]
rs975496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs991145	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758047	chr6:35168116-35291002	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	esv2759419	chr6:35168116-35291002	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9380501	DEF6	cis	multi-tissue	Pritchard
rs9380501	ENSG00000023892	cis	multi-tissue	Pritchard

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35263200-35270600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr6:35263200-35270600	Weak transcription	NHDF-Ad	bronchial
3	chr6:35265200-35270600	Weak transcription	HSMM	muscle
4	chr6:35265200-35285600	Weak transcription	Brain Substantia Nigra	brain
5	chr6:35265400-35272200	Weak transcription	Fetal Brain Female	brain
6	chr6:35266000-35270800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr6:35266000-35271000	Weak transcription	Left Ventricle	heart
8	chr6:35266000-35271000	Weak transcription	Right Ventricle	heart
9	chr6:35266000-35272000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr6:35266200-35270600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:35266200-35270800	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr6:35266400-35270600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr6:35266400-35270600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr6:35266400-35270600	Weak transcription	HUVEC	blood vessel
15	chr6:35266600-35270600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr6:35266600-35270800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
17	chr6:35266600-35272000	Weak transcription	Gastric	stomach
18	chr6:35266600-35279800	Weak transcription	Fetal Stomach	stomach
19	chr6:35266800-35277400	Weak transcription	Pancreas	Pancrea
20	chr6:35267400-35272400	Enhancers	Small Intestine	intestine
21	chr6:35268400-35270600	Enhancers	Primary B cells from peripheral blood	blood
22	chr6:35268600-35271000	Enhancers	Primary hematopoietic stem cells	blood
23	chr6:35268600-35278600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr6:35268800-35270600	Weak transcription	Colonic Mucosa	Colon
25	chr6:35269000-35272400	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr6:35269200-35270800	Genic enhancers	Fetal Thymus	thymus
27	chr6:35269200-35273200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:35269600-35270600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr6:35269600-35270600	Enhancers	Stomach Mucosa	stomach
30	chr6:35269800-35270600	Enhancers	Esophagus	oesophagus
31	chr6:35269800-35270600	Genic enhancers	Placenta	Placenta
32	chr6:35269800-35271000	Enhancers	Lung	lung
33	chr6:35269800-35271400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
34	chr6:35269800-35272200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
35	chr6:35270000-35270600	Enhancers	Duodenum Mucosa	Duodenum
36	chr6:35270000-35270600	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr6:35270000-35270600	Enhancers	HMEC	breast
38	chr6:35270000-35270800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
39	chr6:35270000-35271200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr6:35270000-35271400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
41	chr6:35270000-35271400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr6:35270000-35271600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
43	chr6:35270000-35271600	Enhancers	Fetal Intestine Small	intestine
44	chr6:35270000-35272200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr6:35270000-35272200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
46	chr6:35270200-35270600	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr6:35270200-35270600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
48	chr6:35270200-35270800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr6:35270200-35270800	Enhancers	K562	blood
50	chr6:35270200-35270800	Enhancers	Osteobl	bone

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