Variant report

Variant	rs2759389
Chromosome Location	chr6:163912700-163912701
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:163906576..163909444-chr6:163912230..163915189,4	K562	blood:

Extended variants
information (count: 135 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs1003528	1.00[ASN][1000 genomes]
rs1016501	0.82[CEU][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1016502	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1040514	1.00[CEU][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1047944	1.00[ASN][1000 genomes]
rs11752044	1.00[ASN][1000 genomes]
rs12194023	1.00[ASN][1000 genomes]
rs1230321	1.00[ASN][1000 genomes]
rs1234603	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1234604	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs1234976	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1238371	0.86[EUR][1000 genomes]
rs1614795	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1619076	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1619863	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1629251	1.00[ASN][1000 genomes]
rs1737329	1.00[ASN][1000 genomes]
rs1737333	1.00[ASN][1000 genomes]
rs1737600	1.00[ASN][1000 genomes]
rs1737601	0.95[CEU][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1737603	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1737604	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1737606	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1737607	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs1737609	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1737611	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1737612	1.00[ASN][1000 genomes]
rs1744924	1.00[CEU][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]
rs1744925	0.95[CEU][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1744926	0.82[CEU][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1744927	0.82[CEU][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1744928	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1744933	0.82[CEU][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1745094	1.00[ASN][1000 genomes]
rs2038146	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2038147	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2038148	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2057003	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2092406	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2092407	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2103671	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2179523	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2179524	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2321698	1.00[ASN][1000 genomes]
rs2321700	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2321701	1.00[ASN][1000 genomes]
rs2321702	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2484877	1.00[ASN][1000 genomes]
rs2744420	1.00[ASN][1000 genomes]
rs2744421	1.00[ASN][1000 genomes]
rs2745364	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2745365	1.00[ASN][1000 genomes]
rs2757579	1.00[ASN][1000 genomes]
rs2757580	1.00[ASN][1000 genomes]
rs2757581	1.00[ASN][1000 genomes]
rs2757582	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2757583	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2757586	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2757587	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2757589	0.90[CEU][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2759381	0.82[CEU][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2759382	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2759383	0.86[CEU][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2759384	0.90[CEU][hapmap];0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2759385	1.00[ASN][1000 genomes]
rs2759387	0.86[CEU][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2759388	1.00[ASN][1000 genomes]
rs2759390	1.00[ASN][1000 genomes]
rs2759391	1.00[ASN][1000 genomes]
rs2759392	1.00[ASN][1000 genomes]
rs2759393	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2759395	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2759398	1.00[ASN][1000 genomes]
rs2759399	1.00[ASN][1000 genomes]
rs2784865	1.00[ASN][1000 genomes]
rs2784867	1.00[ASN][1000 genomes]
rs2784873	1.00[ASN][1000 genomes]
rs2874602	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4708996	1.00[ASN][1000 genomes]
rs4708997	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56721804	1.00[ASN][1000 genomes]
rs6455900	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6455901	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6455902	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6455903	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6455904	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6905852	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6906008	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6909364	1.00[CEU][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6913113	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6914387	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6915247	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6924130	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6926584	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6927417	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6931049	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs721190	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs721191	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7746116	1.00[ASN][1000 genomes]
rs7749189	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7751784	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7752945	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs7761088	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7768051	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7769145	0.95[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7775850	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7776279	1.00[ASN][1000 genomes]
rs783136	1.00[ASN][1000 genomes]
rs783138	0.90[CEU][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs783140	0.90[CEU][hapmap];1.00[ASN][1000 genomes]
rs803613	1.00[ASN][1000 genomes]
rs809155	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs813640	1.00[ASN][1000 genomes]
rs814143	0.86[CEU][hapmap];0.88[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295222	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295223	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295224	1.00[ASN][1000 genomes]
rs9347754	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9347755	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9347756	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9347759	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9347763	1.00[ASN][1000 genomes]
rs9356117	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9356120	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9356121	1.00[ASN][1000 genomes]
rs9365572	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9365573	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9365574	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9365577	1.00[ASN][1000 genomes]
rs9456866	1.00[CEU][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9456869	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932127	chr6:163000261-163950870	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv534621	chr6:163731741-163950870	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1019551	chr6:163842358-163965216	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2759389	QKI	cis	uninvolved skin	skin_eQTL
rs2759389	QKI	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163893000-163912800	Weak transcription	Fetal Brain Male	brain
2	chr6:163898400-163926000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:163902200-163913600	Enhancers	Brain Anterior Caudate	brain
4	chr6:163902600-163921800	Weak transcription	HepG2	liver
5	chr6:163903000-163915000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr6:163903000-163924200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr6:163903600-163926000	Weak transcription	Lung	lung
8	chr6:163904000-163917400	Weak transcription	Fetal Muscle Leg	muscle
9	chr6:163905000-163918400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr6:163905200-163915400	Enhancers	Fetal Heart	heart
11	chr6:163905800-163921800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr6:163906800-163916800	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr6:163906800-163919400	Weak transcription	Ovary	ovary
14	chr6:163907000-163913400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr6:163907200-163915400	Weak transcription	Right Ventricle	heart
16	chr6:163907200-163925000	Weak transcription	Fetal Muscle Trunk	muscle
17	chr6:163907200-163926000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr6:163907600-163913200	Enhancers	Brain Cingulate Gyrus	brain
19	chr6:163908600-163917200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr6:163908800-163915000	Weak transcription	GM12878-XiMat	blood
21	chr6:163909200-163921000	Weak transcription	Primary B cells from cord blood	blood
22	chr6:163909400-163913200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr6:163909400-163923800	Weak transcription	Aorta	Aorta
24	chr6:163909600-163922600	Weak transcription	Fetal Brain Female	brain
25	chr6:163910000-163913200	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr6:163910200-163913000	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr6:163910400-163913000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr6:163910400-163913000	Enhancers	Dnd41	blood
29	chr6:163910400-163913200	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr6:163910600-163914200	Weak transcription	Left Ventricle	heart
31	chr6:163910600-163915200	Weak transcription	Right Atrium	heart
32	chr6:163910800-163912800	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr6:163910800-163913000	Enhancers	HUVEC	blood vessel
34	chr6:163910800-163915200	Weak transcription	NHDF-Ad	bronchial
35	chr6:163911200-163917600	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr6:163911200-163926000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr6:163911200-163926200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr6:163911400-163912800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr6:163911400-163913200	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr6:163911600-163913600	Enhancers	Brain Hippocampus Middle	brain
41	chr6:163911600-163928000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr6:163911800-163912800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr6:163911800-163914600	Weak transcription	Psoas Muscle	Psoas
44	chr6:163911800-163914600	Weak transcription	K562	blood
45	chr6:163911800-163915400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr6:163911800-163915400	Weak transcription	HSMM	muscle
47	chr6:163911800-163917000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr6:163911800-163934800	Weak transcription	Pancreas	Pancrea
49	chr6:163912000-163913000	Enhancers	Colon Smooth Muscle	Colon
50	chr6:163912000-163913200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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