Variant report

Variant	rs2757589
Chromosome Location	chr6:163843218-163843219
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:163840864..163843794-chr6:163863418..163865440,3	K562	blood:
2	chr6:163841678..163843266-chr6:163843720..163845491,2	K562	blood:
3	chr6:163838995..163843341-chr6:163850269..163853237,5	K562	blood:
4	chr6:163841069..163843300-chr6:163990563..163993244,2	K562	blood:
5	chr6:163842546..163846148-chr6:163847006..163850145,4	K562	blood:

Variant related genes	Relation type
ENSG00000112531	Chromatin interaction

Extended variants
information (count: 139 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:135)

rs_ID	r²[population]
rs1003528	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1016501	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1016502	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1040514	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1047944	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11752044	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12194023	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1230321	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1234603	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1234604	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1234976	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1614795	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1619076	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1619863	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1629251	0.82[CEU][hapmap];1.00[CHB][hapmap];0.86[TSI][hapmap];1.00[ASN][1000 genomes]
rs1737317	1.00[CHB][hapmap]
rs1737323	1.00[CHB][hapmap]
rs1737329	0.87[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1737333	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1737600	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1737601	0.87[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1737603	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1737604	0.89[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1737606	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1737607	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1737609	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1737611	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1737612	1.00[ASN][1000 genomes]
rs1744924	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1744925	0.86[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1744926	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1744927	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1744928	1.00[ASN][1000 genomes]
rs1744933	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1745094	1.00[ASN][1000 genomes]
rs1764008	1.00[CHB][hapmap]
rs2038146	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2038147	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2038148	0.91[CEU][hapmap];1.00[GIH][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs2057003	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs2092406	0.90[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2092407	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2103671	0.83[EUR][1000 genomes]
rs2179523	1.00[ASN][1000 genomes]
rs2179524	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2321698	1.00[ASN][1000 genomes]
rs2321700	1.00[ASN][1000 genomes]
rs2321701	1.00[ASN][1000 genomes]
rs2321702	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.81[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	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2745365	1.00[ASN][1000 genomes]
rs2757579	1.00[ASN][1000 genomes]
rs2757580	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2757581	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2757582	1.00[ASN][1000 genomes]
rs2757583	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2757586	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2757587	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2757588	1.00[CHB][hapmap]
rs2759381	0.82[CEU][hapmap];1.00[ASN][1000 genomes]
rs2759382	0.82[EUR][1000 genomes]
rs2759383	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2759384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2759385	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2759387	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2759388	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2759389	0.90[CEU][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2759390	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2759391	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2759392	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2759393	0.91[CEU][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2759395	0.91[CEU][hapmap];1.00[CHB][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2759398	1.00[ASN][1000 genomes]
rs2759399	1.00[ASN][1000 genomes]
rs2784865	0.87[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2784867	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2784873	1.00[ASN][1000 genomes]
rs2784874	1.00[CHB][hapmap]
rs2874602	0.91[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4708996	1.00[ASN][1000 genomes]
rs4708997	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs56721804	1.00[ASN][1000 genomes]
rs6455900	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6455902	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6455903	0.90[CEU][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6455904	1.00[ASN][1000 genomes]
rs6905852	0.82[EUR][1000 genomes]
rs6906008	0.82[EUR][1000 genomes]
rs6909364	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6913113	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6914387	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6915247	0.91[CEU][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6924130	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6926584	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6927417	1.00[ASN][1000 genomes]
rs6931049	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs721190	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs721191	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7746116	1.00[ASN][1000 genomes]
rs7749189	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7752945	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7761088	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7768051	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7769145	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7775850	1.00[ASN][1000 genomes]
rs7776279	1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[ASN][1000 genomes]
rs783136	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs783138	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs783140	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs803613	1.00[ASN][1000 genomes]
rs809155	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs813640	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs814143	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295222	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295223	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9295224	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9347754	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9347755	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9347756	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9347759	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9347763	1.00[ASN][1000 genomes]
rs9355427	1.00[CHB][hapmap]
rs9356117	0.89[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9356119	1.00[CHB][hapmap]
rs9356120	1.00[ASN][1000 genomes]
rs9356121	1.00[ASN][1000 genomes]
rs9365572	0.89[CEU][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9365573	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9365574	0.91[CEU][hapmap];1.00[ASN][1000 genomes]
rs9365577	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9456866	0.90[CEU][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9456869	0.91[CEU][hapmap];1.00[CHB][hapmap];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	esv1797109	chr6:163834147-163908115	Genic enhancers Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2757589	QKI	Cis_1M	lymphoblastoid	RTeQTL
rs2757589	QKI	cis	uninvolved skin	skin_eQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163833000-163843400	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr6:163833400-163843600	Active TSS	Right Ventricle	heart
3	chr6:163836200-163843400	Active TSS	Brain Angular Gyrus	brain
4	chr6:163837000-163843400	Active TSS	Right Atrium	heart
5	chr6:163837400-163857200	Weak transcription	Spleen	Spleen
6	chr6:163837800-163843400	Weak transcription	Gastric	stomach
7	chr6:163837800-163851000	Weak transcription	Small Intestine	intestine
8	chr6:163838000-163843400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr6:163838000-163843400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr6:163838000-163843600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr6:163838000-163843600	Weak transcription	Esophagus	oesophagus
12	chr6:163838000-163843800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr6:163838000-163847600	Weak transcription	Pancreas	Pancrea
14	chr6:163838000-163851600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:163838000-163860600	Weak transcription	Primary B cells from peripheral blood	blood
16	chr6:163838400-163845000	Weak transcription	Placenta	Placenta
17	chr6:163838800-163845200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr6:163839200-163845400	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr6:163839600-163846200	Weak transcription	Thymus	Thymus
20	chr6:163839800-163851600	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr6:163840000-163845000	Enhancers	Colon Smooth Muscle	Colon
22	chr6:163840200-163844800	Weak transcription	Hela-S3	cervix
23	chr6:163840200-163844800	Enhancers	HepG2	liver
24	chr6:163840800-163865000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr6:163840800-163881400	Weak transcription	Fetal Stomach	stomach
26	chr6:163841000-163847600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr6:163841200-163843400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr6:163841200-163843600	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr6:163841200-163843600	Weak transcription	Primary B cells from cord blood	blood
30	chr6:163841600-163843400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr6:163841600-163843400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr6:163841600-163843600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr6:163841600-163843600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr6:163841600-163843600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr6:163841600-163843600	Weak transcription	NHDF-Ad	bronchial
36	chr6:163841600-163844400	Weak transcription	NHLF	lung
37	chr6:163841600-163845800	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr6:163841600-163847400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr6:163841600-163847400	Weak transcription	Aorta	Aorta
40	chr6:163841600-163848000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr6:163841600-163848600	Weak transcription	HMEC	breast
42	chr6:163841600-163853200	Enhancers	Adipose Nuclei	Adipose
43	chr6:163841600-163858600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr6:163841600-163864400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr6:163841800-163843600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr6:163841800-163843600	Active TSS	Brain Substantia Nigra	brain
47	chr6:163841800-163843600	Weak transcription	NHEK	skin
48	chr6:163841800-163843600	Weak transcription	Osteobl	bone
49	chr6:163841800-163844000	Enhancers	Liver	Liver
50	chr6:163841800-163845600	Weak transcription	Primary T helper cells fromperipheralblood	blood

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