Variant report

Variant	rs2475390
Chromosome Location	chr6:163849630-163849631
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	CEBPB	chr6:163848822-163849773	K562	blood:	n/a	chr6:163848972-163848983 chr6:163849088-163849099
2	CEBPB	chr6:163848842-163849777	IMR90	lung:	n/a	chr6:163848972-163848983 chr6:163849088-163849099
3	CEBPB	chr6:163849483-163849778	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:163846486..163849719-chr6:163934600..163936577,3	K562	blood:
2	chr6:163833988..163836212-chr6:163848529..163850044,2	MCF-7	breast:
3	chr6:163842546..163846148-chr6:163847006..163850145,4	K562	blood:

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

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12210561	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1230320	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1234977	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1572434	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1614869	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1737330	0.85[EUR][1000 genomes]
rs1737610	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1744929	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1764022	0.85[EUR][1000 genomes]
rs1764023	0.85[EUR][1000 genomes]
rs2259476	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2259477	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2475877	0.87[EUR][1000 genomes]
rs2757575	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2757576	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2757584	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2757585	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2759386	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2759396	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6939187	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73021476	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs783137	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs783139	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs803612	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9347747	0.87[EUR][1000 genomes]
rs9347752	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9347765	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9347766	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9365575	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9458843	0.84[AMR][1000 genomes];0.89[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2475390	QKI	cis	Whole Blood	GTEx

Chromatin state (count:96 , 50 per page) page: 1 2

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	chr6:163838000-163851600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:163838000-163860600	Weak transcription	Primary B cells from peripheral blood	blood
5	chr6:163839800-163851600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr6:163840800-163865000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr6:163840800-163881400	Weak transcription	Fetal Stomach	stomach
8	chr6:163841600-163853200	Enhancers	Adipose Nuclei	Adipose
9	chr6:163841600-163858600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:163841600-163864400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr6:163841800-163851000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr6:163842000-163850000	Weak transcription	HSMMtube	muscle
13	chr6:163842200-163851000	Weak transcription	Primary hematopoietic stem cells	blood
14	chr6:163842400-163849800	Weak transcription	Primary T cells from cord blood	blood
15	chr6:163842600-163865200	Weak transcription	Fetal Kidney	kidney
16	chr6:163843800-163856200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr6:163843800-163862600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr6:163844200-163853600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr6:163844200-163860400	Weak transcription	Lung	lung
20	chr6:163844600-163850800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr6:163844600-163851000	Weak transcription	Gastric	stomach
22	chr6:163845400-163851600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr6:163845400-163877800	Weak transcription	Fetal Muscle Leg	muscle
24	chr6:163846000-163850000	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr6:163846000-163861600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr6:163846400-163849800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr6:163846400-163850800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr6:163846400-163851000	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr6:163846400-163860000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr6:163847000-163853200	Enhancers	Liver	Liver
31	chr6:163847200-163850600	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr6:163847400-163852000	Enhancers	Rectal Smooth Muscle	rectum
33	chr6:163847400-163852600	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr6:163847400-163853200	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr6:163847600-163853200	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr6:163847800-163849800	Weak transcription	Fetal Brain Female	brain
37	chr6:163847800-163850600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr6:163847800-163851000	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr6:163847800-163851000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr6:163847800-163853000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr6:163847800-163862400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr6:163847800-163862600	Weak transcription	Aorta	Aorta
43	chr6:163848000-163850000	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr6:163848000-163850200	Enhancers	Fetal Lung	lung
45	chr6:163848000-163850800	Enhancers	Fetal Brain Male	brain
46	chr6:163848000-163851000	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr6:163848200-163850400	Enhancers	HSMM	muscle
48	chr6:163848200-163850800	Weak transcription	NHEK	skin
49	chr6:163848200-163852200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr6:163848200-163853400	Weak transcription	Left Ventricle	heart

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