Variant report

Variant	rs2757588
Chromosome Location	chr6:163846855-163846856
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:163846796-163846941	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:163846486..163849719-chr6:163934600..163936577,3	K562	blood:
2	chr6:163846244..163848845-chr6:163849876..163852594,2	MCF-7	breast:
3	chr6:163844662..163847045-chr6:163859401..163861276,2	MCF-7	breast:
4	chr6:163832148..163835093-chr6:163846269..163848016,2	MCF-7	breast:
5	chr6:163837219..163840006-chr6:163844641..163847487,2	K562	blood:

No data

Variant related genes	Relation type
QKI	TF binding region
ENSG00000270419	Chromatin interaction
ENSG00000112531	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs1003528	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs1016501	1.00[CHB][hapmap]
rs1016502	1.00[CHB][hapmap]
rs1040514	1.00[CHB][hapmap]
rs1047944	0.88[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs1230321	0.89[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1234603	1.00[CHB][hapmap]
rs1234604	1.00[CHB][hapmap]
rs1619076	1.00[CHB][hapmap]
rs1629251	1.00[CHB][hapmap]
rs1737317	1.00[CHB][hapmap]
rs1737323	1.00[CHB][hapmap]
rs1737329	1.00[CHB][hapmap]
rs1737333	1.00[CHB][hapmap]
rs1737600	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs1737601	1.00[CHB][hapmap]
rs1737603	1.00[CHB][hapmap]
rs1737604	1.00[CHB][hapmap]
rs1737606	1.00[CHB][hapmap]
rs1737607	1.00[CHB][hapmap]
rs1737611	1.00[CHB][hapmap]
rs1737612	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1744924	1.00[CHB][hapmap]
rs1744925	1.00[CHB][hapmap]
rs1744926	1.00[CHB][hapmap]
rs1744927	1.00[CHB][hapmap]
rs1744933	1.00[CHB][hapmap]
rs1745094	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs1764008	1.00[CHB][hapmap]
rs2038147	1.00[CHB][hapmap]
rs2057003	1.00[CHB][hapmap]
rs2092406	1.00[CHB][hapmap]
rs2179524	1.00[CHB][hapmap]
rs2321701	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs2321702	1.00[CHB][hapmap]
rs2484877	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2745364	1.00[CHB][hapmap]
rs2745365	0.86[EUR][1000 genomes]
rs2757578	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2757579	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2757580	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2757581	1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2757586	1.00[CHB][hapmap]
rs2757587	1.00[CHB][hapmap]
rs2757589	1.00[CHB][hapmap]
rs2759383	1.00[CHB][hapmap]
rs2759384	1.00[CHB][hapmap]
rs2759385	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2759387	1.00[CHB][hapmap]
rs2759388	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]
rs2759390	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2759391	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2759392	1.00[CHB][hapmap]
rs2759395	1.00[CHB][hapmap]
rs2759398	0.88[EUR][1000 genomes]
rs2759399	0.88[EUR][1000 genomes]
rs2784865	1.00[CHB][hapmap]
rs2784867	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2784874	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs2874602	1.00[CHB][hapmap]
rs4708996	0.84[EUR][1000 genomes]
rs4708997	1.00[CHB][hapmap]
rs5008180	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6455902	1.00[CHB][hapmap]
rs6909364	1.00[CHB][hapmap]
rs6914387	1.00[CHB][hapmap]
rs6924130	1.00[CHB][hapmap]
rs6926584	1.00[CHB][hapmap]
rs6931049	1.00[CHB][hapmap]
rs721190	1.00[CHB][hapmap]
rs721191	1.00[CHB][hapmap]
rs7746116	0.82[EUR][1000 genomes]
rs7749189	1.00[CHB][hapmap]
rs7752945	1.00[CHB][hapmap]
rs7761088	1.00[CHB][hapmap]
rs7768051	1.00[CHB][hapmap]
rs7769145	1.00[CHB][hapmap]
rs7776279	1.00[CHB][hapmap]
rs783136	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs783138	1.00[CHB][hapmap]
rs783140	1.00[CHB][hapmap]
rs803613	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs813640	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs814143	1.00[CHB][hapmap]
rs9295222	1.00[CHB][hapmap]
rs9295223	1.00[CHB][hapmap]
rs9295224	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs9347754	1.00[CHB][hapmap]
rs9347755	1.00[CHB][hapmap]
rs9347756	1.00[CHB][hapmap]
rs9347763	0.81[EUR][1000 genomes]
rs9355427	1.00[CHB][hapmap]
rs9356117	1.00[CHB][hapmap]
rs9356119	1.00[CHB][hapmap]
rs9365573	1.00[CHB][hapmap]
rs9365577	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs9456869	1.00[CHB][hapmap]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2757588	QKI	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163837400-163857200	Weak transcription	Spleen	Spleen
2	chr6:163837800-163851000	Weak transcription	Small Intestine	intestine
3	chr6:163838000-163847600	Weak transcription	Pancreas	Pancrea
4	chr6:163838000-163851600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:163838000-163860600	Weak transcription	Primary B cells from peripheral blood	blood
6	chr6:163839800-163851600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr6:163840800-163865000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr6:163840800-163881400	Weak transcription	Fetal Stomach	stomach
9	chr6:163841000-163847600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr6:163841600-163847400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr6:163841600-163847400	Weak transcription	Aorta	Aorta
12	chr6:163841600-163848000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr6:163841600-163848600	Weak transcription	HMEC	breast
14	chr6:163841600-163853200	Enhancers	Adipose Nuclei	Adipose
15	chr6:163841600-163858600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:163841600-163864400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr6:163841800-163848600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr6:163841800-163851000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr6:163842000-163847600	Enhancers	Fetal Brain Male	brain
20	chr6:163842000-163848200	Weak transcription	GM12878-XiMat	blood
21	chr6:163842000-163850000	Weak transcription	HSMMtube	muscle
22	chr6:163842200-163851000	Weak transcription	Primary hematopoietic stem cells	blood
23	chr6:163842400-163847200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr6:163842400-163848000	Weak transcription	Fetal Lung	lung
25	chr6:163842400-163849800	Weak transcription	Primary T cells from cord blood	blood
26	chr6:163842600-163847400	Weak transcription	HUVEC	blood vessel
27	chr6:163842600-163865200	Weak transcription	Fetal Kidney	kidney
28	chr6:163843200-163848600	Weak transcription	Fetal Muscle Trunk	muscle
29	chr6:163843800-163856200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr6:163843800-163862600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr6:163844000-163847200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr6:163844200-163847400	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr6:163844200-163847600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr6:163844200-163848000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr6:163844200-163853600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr6:163844200-163860400	Weak transcription	Lung	lung
37	chr6:163844600-163847400	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr6:163844600-163847600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr6:163844600-163848000	Enhancers	Monocytes-CD14+_RO01746	blood
40	chr6:163844600-163848600	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr6:163844600-163848800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr6:163844600-163850800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr6:163844600-163851000	Weak transcription	Gastric	stomach
44	chr6:163844800-163847200	Weak transcription	HepG2	liver
45	chr6:163844800-163847400	Weak transcription	HSMM	muscle
46	chr6:163844800-163849200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr6:163845000-163848600	Weak transcription	A549	lung
48	chr6:163845200-163847400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr6:163845200-163847400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr6:163845200-163847400	Weak transcription	NHEK	skin

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