Variant report

Variant	rs2759388
Chromosome Location	chr6:163838794-163838795
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ARID3A	chr6:163837789-163839034	K562	blood:	n/a	chr6:163838362-163838378
2	TBL1XR1	chr6:163836856-163839187	K562	blood:	n/a	n/a
3	TAL1	chr6:163838349-163838910	K562	blood:	n/a	chr6:163838877-163838895
4	STAT3	chr6:163838744-163839140	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr6:163838457-163839081	MCF10A-Er-Src	breast:	n/a	chr6:163838660-163838667
6	ZNF384	chr6:163836894-163839662	K562	blood:	n/a	n/a
7	CTCF	chr6:163838700-163838850	AG09319	gingival:	n/a	n/a
8	CHD1	chr6:163835594-163839152	IMR90	lung:	n/a	n/a
9	MYC	chr6:163838762-163839054	MCF10A-Er-Src	breast:	n/a	n/a
10	IRF1	chr6:163836838-163839596	K562	blood:	n/a	chr6:163837498-163837512 chr6:163837425-163837441 chr6:163837502-163837512 chr6:163837502-163837516 chr6:163837499-163837516 chr6:163837500-163837513 chr6:163837499-163837513 chr6:163837496-163837510 chr6:163837494-163837514 chr6:163837502-163837513 chr6:163837500-163837513 chr6:163838093-163838100
11	EBF1	chr6:163838693-163838995	GM12878	blood:	n/a	n/a
12	ARID3A	chr6:163837700-163839123	HepG2	liver:	n/a	chr6:163838362-163838378
13	FOS	chr6:163838723-163839087	MCF10A-Er-Src	breast:	n/a	n/a
14	CUX1	chr6:163837628-163839565	K562	blood:	n/a	chr6:163839091-163839105 chr6:163839088-163839104
15	UBTF	chr6:163838637-163838872	K562	blood:	n/a	n/a
16	POLR2A	chr6:163836780-163838958	MCF10A-Er-Src	breast:	n/a	n/a
17	FOS	chr6:163838651-163838890	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:163838578..163840743-chr6:164003751..164005658,2	K562	blood:
2	chr6:163836144..163840696-chr6:163983068..163987938,4	K562	blood:
3	chr6:163837764..163839976-chr6:164521625..164524241,2	K562	blood:

Variant related genes	Relation type
CAHM	TF binding region
ENSG00000112531	Chromatin interaction

Extended variants
information (count: 142 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:132)

rs_ID	r²[population]
rs1003528	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1016501	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1016502	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1040514	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1047944	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11752044	1.00[ASN][1000 genomes]
rs12194023	1.00[ASN][1000 genomes]
rs1230321	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1234603	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1234604	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1234976	1.00[ASN][1000 genomes]
rs1614795	1.00[ASN][1000 genomes]
rs1619076	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1619863	1.00[ASN][1000 genomes]
rs1629251	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1737317	1.00[CHB][hapmap]
rs1737323	1.00[CHB][hapmap]
rs1737329	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1737333	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1737600	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1737601	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1737603	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1737604	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1737606	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1737607	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1737609	1.00[ASN][1000 genomes]
rs1737611	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1737612	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1744924	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1744925	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1744926	1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[ASN][1000 genomes]
rs1744927	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1744928	0.81[YRI][hapmap];1.00[ASN][1000 genomes]
rs1744933	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1745094	0.92[CEU][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1764008	1.00[CHB][hapmap]
rs2038146	1.00[ASN][1000 genomes]
rs2038147	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2057003	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2092406	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2092407	1.00[ASN][1000 genomes]
rs2179523	1.00[ASN][1000 genomes]
rs2179524	1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[ASN][1000 genomes]
rs2321698	1.00[ASN][1000 genomes]
rs2321700	1.00[ASN][1000 genomes]
rs2321701	0.88[CEU][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2321702	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2484877	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744420	1.00[ASN][1000 genomes]
rs2744421	1.00[ASN][1000 genomes]
rs2745364	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2745365	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2757578	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2757579	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2757580	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2757581	1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2757582	1.00[ASN][1000 genomes]
rs2757583	1.00[ASN][1000 genomes]
rs2757586	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2757587	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2757588	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2757589	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2759381	1.00[ASN][1000 genomes]
rs2759383	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2759384	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2759385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2759387	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2759389	1.00[ASN][1000 genomes]
rs2759390	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2759391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2759392	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2759393	1.00[ASN][1000 genomes]
rs2759395	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2759398	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2759399	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2784865	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2784867	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2784873	1.00[ASN][1000 genomes]
rs2784874	0.81[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];0.88[TSI][hapmap]
rs2874602	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4708996	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4708997	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs5008180	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56721804	1.00[ASN][1000 genomes]
rs6455900	1.00[ASN][1000 genomes]
rs6455902	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6455903	1.00[ASN][1000 genomes]
rs6455904	1.00[ASN][1000 genomes]
rs6909364	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6913113	1.00[ASN][1000 genomes]
rs6914387	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6915247	1.00[ASN][1000 genomes]
rs6924130	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6926584	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6927417	1.00[ASN][1000 genomes]
rs6931049	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs721190	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs721191	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7746116	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7749189	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7752945	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7761088	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7768051	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7769145	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7775850	1.00[ASN][1000 genomes]
rs7776279	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs783136	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs783138	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs783140	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs803613	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs809155	1.00[ASN][1000 genomes]
rs813640	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs814143	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9295222	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9295223	1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[ASN][1000 genomes]
rs9295224	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs9347754	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9347755	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9347756	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9347759	1.00[ASN][1000 genomes]
rs9347763	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9355427	1.00[CHB][hapmap]
rs9356117	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9356119	1.00[CHB][hapmap]
rs9356120	1.00[ASN][1000 genomes]
rs9356121	1.00[ASN][1000 genomes]
rs9365572	1.00[ASN][1000 genomes]
rs9365573	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9365574	1.00[ASN][1000 genomes]
rs9365577	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9456866	1.00[ASN][1000 genomes]
rs9456869	1.00[CHB][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	esv1809559	chr6:163834909-163838794	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	esv1819183	chr6:163834909-163838794	Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv1829454	chr6:163834909-163838794	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	esv1841776	chr6:163834909-163838794	Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	esv1851449	chr6:163834909-163838794	Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv605205	chr6:163834909-163838794	Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv605209	chr6:163835281-163839012	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2759388	QKI	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163832600-163841400	Active TSS	Skeletal Muscle Male	skeletal muscle
2	chr6:163833000-163843400	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr6:163833200-163841000	Active TSS	Fetal Muscle Leg	muscle
4	chr6:163833200-163842000	Active TSS	HSMMtube	muscle
5	chr6:163833400-163838800	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr6:163833400-163839400	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr6:163833400-163839400	Active TSS	NH-A	brain
8	chr6:163833400-163839600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr6:163833400-163839800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr6:163833400-163839800	Active TSS	Fetal Muscle Trunk	muscle
11	chr6:163833400-163840400	Active TSS	Fetal Brain Female	brain
12	chr6:163833400-163840600	Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr6:163833400-163841400	Active TSS	Stomach Smooth Muscle	stomach
14	chr6:163833400-163841400	Active TSS	NHLF	lung
15	chr6:163833400-163843600	Active TSS	Right Ventricle	heart
16	chr6:163833600-163838800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
17	chr6:163833600-163838800	Active TSS	Hela-S3	cervix
18	chr6:163833600-163839400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr6:163833600-163839600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
20	chr6:163833600-163840000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr6:163833600-163840400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr6:163833600-163841400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr6:163833600-163841400	Active TSS	HSMM	muscle
24	chr6:163833600-163842400	Active TSS	Psoas Muscle	Psoas
25	chr6:163833600-163843000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr6:163833800-163838800	Active TSS	H1 Cell Line	embryonic stem cell
27	chr6:163833800-163838800	Active TSS	Aorta	Aorta
28	chr6:163833800-163839800	Active TSS	Left Ventricle	heart
29	chr6:163833800-163840000	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr6:163833800-163840800	Active TSS	K562	blood
31	chr6:163833800-163841600	Active TSS	Ovary	ovary
32	chr6:163834000-163839000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
33	chr6:163834000-163839000	Active TSS	NHEK	skin
34	chr6:163834000-163840800	Active TSS	GM12878-XiMat	blood
35	chr6:163834200-163838800	Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr6:163834200-163838800	Active TSS	iPS-15b Cell Line	embryonic stem cell
37	chr6:163834200-163838800	Active TSS	Primary monocytes fromperipheralblood	blood
38	chr6:163834200-163838800	Active TSS	Muscle Satellite Cultured Cells	--
39	chr6:163834200-163838800	Active TSS	Fetal Stomach	stomach
40	chr6:163834200-163839200	Active TSS	Thymus	Thymus
41	chr6:163834200-163839400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr6:163834200-163839400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr6:163834200-163841000	Active TSS	HMEC	breast
44	chr6:163834200-163841400	Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr6:163834400-163838800	Active TSS	HUVEC	blood vessel
46	chr6:163834400-163839000	Active TSS	Osteobl	bone
47	chr6:163835000-163841600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr6:163836200-163838800	Active TSS	A549	lung
49	chr6:163836200-163839600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr6:163836200-163840800	Active TSS	Duodenum Smooth Muscle	Duodenum

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