Variant report

Variant	rs1408493
Chromosome Location	chr6:119588794-119588795
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:119584481..119586279-chr6:119586343..119589172,2	K562	blood:
2	chr6:119585952..119589084-chr6:119590511..119594109,4	K562	blood:
3	chr6:119585891..119588843-chr6:119590511..119597108,7	K562	blood:

Variant related genes	Relation type
ENSG00000216316	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1076656	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1104741	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11153798	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11153801	0.85[ASN][1000 genomes]
rs11153802	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11755686	0.85[ASN][1000 genomes]
rs11962211	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12207164	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12211868	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1408491	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1408492	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1555683	0.84[ASN][1000 genomes]
rs195046	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs195051	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs195062	0.91[EUR][1000 genomes]
rs195079	0.87[EUR][1000 genomes]
rs195083	0.86[EUR][1000 genomes]
rs195088	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs195091	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2064160	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2093906	0.88[AMR][1000 genomes]
rs2142885	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2142890	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2267672	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2299879	0.84[ASN][1000 genomes]
rs2299881	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2299884	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2357162	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2357163	0.83[ASN][1000 genomes]
rs2357375	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3798609	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3798616	0.83[ASN][1000 genomes]
rs3822997	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4945633	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4945634	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4946406	0.88[AFR][1000 genomes]
rs6569060	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6569061	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6569063	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6569074	0.81[EUR][1000 genomes]
rs6933914	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7357047	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7357048	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs763293	0.83[ASN][1000 genomes]
rs7775421	0.83[EUR][1000 genomes]
rs9320684	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9385068	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9489625	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9489627	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9489628	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9489633	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9489637	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9489654	0.90[ASN][1000 genomes]
rs980818	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs998194	0.83[EUR][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	nsv1025995	chr6:119407742-119709548	Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv886570	chr6:119450888-119600556	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1017507	chr6:119465981-119664949	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	esv3447598	chr6:119558591-120119384	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	esv3389526	chr6:119558598-120190087	ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119558800-119589800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:119558800-119590200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:119558800-119590400	Weak transcription	GM12878-XiMat	blood
4	chr6:119558800-119602000	Weak transcription	Gastric	stomach
5	chr6:119562800-119590200	Weak transcription	Fetal Stomach	stomach
6	chr6:119562800-119590800	Weak transcription	Fetal Muscle Leg	muscle
7	chr6:119563400-119590200	Weak transcription	Stomach Smooth Muscle	stomach
8	chr6:119568600-119592600	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr6:119569200-119589800	Weak transcription	Fetal Intestine Large	intestine
10	chr6:119569200-119590000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr6:119569200-119590400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr6:119569200-119591600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr6:119569200-119591600	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr6:119569400-119590000	Weak transcription	Placenta	Placenta
15	chr6:119569400-119590200	Weak transcription	Left Ventricle	heart
16	chr6:119569400-119591600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr6:119574200-119589800	Weak transcription	Fetal Intestine Small	intestine
18	chr6:119577000-119588800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr6:119578600-119588800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr6:119580400-119588800	Weak transcription	Small Intestine	intestine
21	chr6:119581800-119590000	Weak transcription	Adipose Nuclei	Adipose
22	chr6:119582800-119591600	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr6:119583200-119590200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr6:119583400-119589000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr6:119583400-119589600	Weak transcription	Pancreas	Pancrea
26	chr6:119583400-119590000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr6:119583400-119590200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr6:119583400-119590600	Weak transcription	Lung	lung
29	chr6:119583400-119590800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr6:119583400-119591600	Weak transcription	NHDF-Ad	bronchial
31	chr6:119584200-119590000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr6:119584400-119588800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr6:119584400-119588800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr6:119584400-119589400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr6:119584800-119590200	Weak transcription	Primary B cells from cord blood	blood
36	chr6:119585400-119588800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr6:119585600-119591000	Genic enhancers	HepG2	liver
38	chr6:119586000-119588800	Weak transcription	K562	blood
39	chr6:119586400-119591200	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr6:119586600-119590000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr6:119587200-119590200	Weak transcription	Ovary	ovary
42	chr6:119587200-119591800	Weak transcription	Primary B cells from peripheral blood	blood
43	chr6:119587800-119589200	Enhancers	Fetal Lung	lung
44	chr6:119588000-119589000	Enhancers	Fetal Kidney	kidney
45	chr6:119588000-119589800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr6:119588200-119590000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr6:119588200-119590600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr6:119588200-119592000	Strong transcription	Liver	Liver
49	chr6:119588400-119589000	Weak transcription	Colon Smooth Muscle	Colon
50	chr6:119588400-119589800	Enhancers	Primary T cells from cord blood	blood

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