Variant report

Variant	rs1238371
Chromosome Location	chr6:163966888-163966889
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:163959475..163961501-chr6:163964972..163967917,2	K562	blood:
2	chr6:163889319..163891540-chr6:163964872..163967579,2	K562	blood:
3	chr6:163965536..163967717-chr6:163977129..163979848,2	K562	blood:
4	chr6:163963165..163965030-chr6:163966469..163968182,2	K562	blood:

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1016502	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1040514	0.86[EUR][1000 genomes]
rs1234603	0.83[EUR][1000 genomes]
rs1234976	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1614795	0.86[EUR][1000 genomes]
rs1619076	0.86[EUR][1000 genomes]
rs1619863	0.86[EUR][1000 genomes]
rs1737601	0.83[EUR][1000 genomes]
rs1737603	0.83[EUR][1000 genomes]
rs1737604	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1737606	0.88[EUR][1000 genomes]
rs1737609	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1744924	0.86[EUR][1000 genomes]
rs1744925	0.83[EUR][1000 genomes]
rs2038146	0.86[EUR][1000 genomes]
rs2038147	0.86[EUR][1000 genomes]
rs2038148	0.86[EUR][1000 genomes]
rs2057003	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2092406	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2092407	0.86[EUR][1000 genomes]
rs2103671	0.86[EUR][1000 genomes]
rs2321702	0.89[EUR][1000 genomes]
rs2745364	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2757586	0.83[EUR][1000 genomes]
rs2757587	0.83[EUR][1000 genomes]
rs2759382	0.85[EUR][1000 genomes]
rs2759389	0.86[EUR][1000 genomes]
rs2759393	0.83[EUR][1000 genomes]
rs2759395	0.83[EUR][1000 genomes]
rs2874602	0.86[EUR][1000 genomes]
rs6455900	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6455902	0.88[EUR][1000 genomes]
rs6455903	0.88[EUR][1000 genomes]
rs6455904	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6905852	0.88[EUR][1000 genomes]
rs6906008	0.88[EUR][1000 genomes]
rs6909364	0.89[EUR][1000 genomes]
rs6913113	0.88[EUR][1000 genomes]
rs6914387	0.88[EUR][1000 genomes]
rs6915247	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6926584	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6927417	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6931049	0.90[EUR][1000 genomes]
rs721190	0.86[EUR][1000 genomes]
rs721191	0.86[EUR][1000 genomes]
rs7749189	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7751784	0.86[EUR][1000 genomes]
rs7761088	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7768051	0.86[EUR][1000 genomes]
rs7769145	0.90[EUR][1000 genomes]
rs9295222	0.88[EUR][1000 genomes]
rs9347754	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9347756	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9347759	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9356117	0.86[EUR][1000 genomes]
rs9365572	0.86[EUR][1000 genomes]
rs9365574	0.90[EUR][1000 genomes]
rs9456866	0.89[EUR][1000 genomes]
rs9456869	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017495	chr6:163856399-163981095	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1018860	chr6:163939347-164532579	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv538526	chr6:163939347-164532579	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1238371	QKI	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163926600-163991800	Weak transcription	Esophagus	oesophagus
2	chr6:163940200-163983000	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr6:163949600-163975200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr6:163949600-163992000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr6:163949600-163995400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr6:163951000-163978800	Weak transcription	Fetal Kidney	kidney
7	chr6:163951200-163993200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr6:163951600-163985800	Weak transcription	Hela-S3	cervix
9	chr6:163951800-163973400	Weak transcription	Fetal Stomach	stomach
10	chr6:163952400-163984400	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr6:163952600-163972000	Weak transcription	Primary T cells from cord blood	blood
12	chr6:163952600-163979600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr6:163952600-163981400	Weak transcription	Pancreas	Pancrea
14	chr6:163952600-163982800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr6:163952600-163996600	Weak transcription	Gastric	stomach
16	chr6:163954000-163968400	Weak transcription	K562	blood
17	chr6:163954000-163979400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr6:163954000-163984200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr6:163954000-163984400	Weak transcription	Aorta	Aorta
20	chr6:163954000-163991600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr6:163954800-163984200	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr6:163955000-163979600	Weak transcription	NHEK	skin
23	chr6:163955200-163984200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr6:163955800-163983000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr6:163955800-163984400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr6:163956000-163968400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr6:163956000-163978000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:163956000-163979400	Weak transcription	NHLF	lung
29	chr6:163956200-163979800	Weak transcription	NHDF-Ad	bronchial
30	chr6:163957800-163982800	Weak transcription	Placenta	Placenta
31	chr6:163957800-163983000	Weak transcription	Osteobl	bone
32	chr6:163958200-163968400	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:163958200-163972200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr6:163958200-163975000	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr6:163958200-163984600	Weak transcription	HMEC	breast
36	chr6:163958200-163991600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr6:163958400-163971400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr6:163958400-163975200	Weak transcription	Fetal Lung	lung
39	chr6:163958400-163984400	Weak transcription	Fetal Thymus	thymus
40	chr6:163958600-163980000	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr6:163958800-163970000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr6:163958800-163979600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr6:163958800-163983000	Weak transcription	NH-A	brain
44	chr6:163959000-163977800	Weak transcription	Primary B cells from peripheral blood	blood
45	chr6:163959200-163968400	Weak transcription	HSMMtube	muscle
46	chr6:163959200-163968600	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr6:163959400-163968400	Weak transcription	GM12878-XiMat	blood
48	chr6:163959400-163974800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr6:163959600-163968400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr6:163959600-163968400	Weak transcription	Fetal Muscle Leg	muscle

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