Variant report

Variant	rs9380500
Chromosome Location	chr6:35266231-35266232
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 132 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs10080361	0.89[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1013907	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10755687	0.83[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10807150	0.89[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10947540	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10947542	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1108709	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1194	0.83[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[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	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1557567	0.89[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1557568	0.89[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1590381	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1888822	0.89[CEU][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1888823	0.83[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1888824	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1888825	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1894650	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1894651	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1894652	0.94[ASN][1000 genomes]
rs1894653	0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1929847	0.83[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1929849	0.83[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1987673	0.89[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2006184	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2018373	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2032538	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2071920	0.89[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2183834	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2267657	0.89[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2267658	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2267660	0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2267661	0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs2267662	0.83[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2267663	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2267664	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2284195	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2395614	0.89[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34156110	0.82[ASN][1000 genomes]
rs3777742	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3777743	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3777744	0.82[JPT][hapmap]
rs3798342	0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3798343	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs3800382	0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3800383	0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3800385	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3800386	0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3800387	0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3800388	0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3800392	0.83[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3800393	0.89[CEU][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3800396	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3800398	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3800399	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3800401	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4583983	0.88[ASN][1000 genomes]
rs4711409	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4711411	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4711413	0.87[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4711414	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713841	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4713845	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4713847	0.85[ASN][1000 genomes]
rs4713848	0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4713850	0.81[ASN][1000 genomes]
rs58925593	0.95[ASN][1000 genomes]
rs62403575	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6457812	0.89[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs68164647	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6902523	0.83[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6906987	0.83[ASN][1000 genomes]
rs6907324	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6907364	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6907573	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6907795	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6913037	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6913475	0.84[ASN][1000 genomes]
rs6913941	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6916364	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6919534	0.83[YRI][hapmap]
rs6920432	0.83[ASN][1000 genomes]
rs6920747	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6927730	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6928769	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6930562	0.86[ASN][1000 genomes]
rs6938946	0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6940375	0.81[EUR][1000 genomes]
rs6941471	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72909061	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7757316	0.83[ASN][1000 genomes]
rs7763946	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7769906	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7772212	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7772302	0.82[ASN][1000 genomes]
rs8205	0.94[CEU][hapmap];0.89[CHB][hapmap];0.81[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs914547	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9296144	0.83[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9296150	0.81[ASN][1000 genomes]
rs9348970	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs9366882	0.89[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9366883	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9366885	0.87[ASN][1000 genomes]
rs9368854	0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9368857	0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9368859	0.84[ASN][1000 genomes]
rs9368860	0.84[ASN][1000 genomes]
rs9380497	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9380498	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9380501	0.83[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9380502	0.90[ASN][1000 genomes]
rs9394283	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9394288	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs9394289	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9462065	0.89[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9462072	0.84[ASN][1000 genomes]
rs9469964	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9469972	0.89[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9469975	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9469979	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9469982	0.94[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9469997	0.81[ASN][1000 genomes]
rs9469998	0.83[ASN][1000 genomes]
rs965272	0.89[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs968828	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs975496	0.83[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs991145	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9380500	DEF6	cis	multi-tissue	Pritchard

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35249000-35266800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr6:35251000-35266800	Weak transcription	Fetal Brain Male	brain
3	chr6:35261200-35270400	Weak transcription	Hela-S3	cervix
4	chr6:35263000-35270400	Weak transcription	A549	lung
5	chr6:35263200-35270600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr6:35263200-35270600	Weak transcription	NHDF-Ad	bronchial
7	chr6:35263400-35270200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:35264400-35267400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:35264600-35270400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr6:35264800-35269400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr6:35265000-35266400	Enhancers	HUVEC	blood vessel
12	chr6:35265000-35266600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
13	chr6:35265000-35268200	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr6:35265000-35268400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
15	chr6:35265000-35269200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr6:35265000-35269400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
17	chr6:35265200-35266400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr6:35265200-35266600	Flanking Active TSS	NHEK	skin
19	chr6:35265200-35266800	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr6:35265200-35266800	Flanking Active TSS	HepG2	liver
21	chr6:35265200-35266800	Flanking Active TSS	K562	blood
22	chr6:35265200-35267800	Weak transcription	Brain Germinal Matrix	brain
23	chr6:35265200-35268200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr6:35265200-35270200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr6:35265200-35270200	Weak transcription	Osteobl	bone
26	chr6:35265200-35270600	Weak transcription	HSMM	muscle
27	chr6:35265200-35285600	Weak transcription	Brain Substantia Nigra	brain
28	chr6:35265400-35266400	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
29	chr6:35265400-35266400	Flanking Active TSS	Fetal Muscle Leg	muscle
30	chr6:35265400-35266400	Flanking Active TSS	Fetal Thymus	thymus
31	chr6:35265400-35266600	Active TSS	Primary T killer memory cells from peripheral blood	blood
32	chr6:35265400-35266600	Active TSS	Esophagus	oesophagus
33	chr6:35265400-35266800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr6:35265400-35266800	Flanking Active TSS	Duodenum Mucosa	Duodenum
35	chr6:35265400-35266800	Active TSS	Thymus	Thymus
36	chr6:35265400-35267200	Active TSS	Colonic Mucosa	Colon
37	chr6:35265400-35268400	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr6:35265400-35268600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
39	chr6:35265400-35268800	Active TSS	Rectal Smooth Muscle	rectum
40	chr6:35265400-35269000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
41	chr6:35265400-35270400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr6:35265400-35272200	Weak transcription	Fetal Brain Female	brain
43	chr6:35265600-35266400	Active TSS	Primary T cells from cord blood	blood
44	chr6:35265600-35266400	Active TSS	Primary T cells fromperipheralblood	blood
45	chr6:35265600-35266400	Active TSS	Primary T helper naive cells from peripheral blood	blood
46	chr6:35265600-35266400	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
47	chr6:35265600-35266400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
48	chr6:35265600-35266400	Active TSS	Brain Cingulate Gyrus	brain
49	chr6:35265600-35266400	Flanking Active TSS	Fetal Intestine Large	intestine
50	chr6:35265600-35266400	Active TSS	Small Intestine	intestine

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