Variant report

Variant	rs239932
Chromosome Location	chr6:167414681-167414682
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	MAX	chr6:167414350-167414687	K562	blood:	n/a	chr6:167414558-167414568
2	MAFK	chr6:167414261-167414699	HepG2	liver:	n/a	chr6:167414658-167414672 chr6:167414275-167414286 chr6:167414660-167414671
3	MAX	chr6:167414401-167414724	NB4	blood:	n/a	chr6:167414558-167414568
4	WRNIP1	chr6:167414420-167414689	GM12878	blood:	n/a	n/a
5	MAFK	chr6:167414248-167414754	HepG2	liver:	n/a	chr6:167414658-167414672 chr6:167414275-167414286 chr6:167414660-167414671
6	MAFK	chr6:167414239-167414718	Hela-S3	cervix:	n/a	chr6:167414658-167414672 chr6:167414275-167414286 chr6:167414660-167414671
7	MAFF	chr6:167413975-167414720	K562	blood:	n/a	chr6:167414434-167414452
8	MXI1	chr6:167414386-167414736	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:167353995..167356024-chr6:167413983..167416895,2	K562	blood:
2	chr6:167368436..167372370-chr6:167409956..167415121,7	MCF-7	breast:
3	chr6:167369620..167371640-chr6:167412068..167415220,3	K562	blood:

Variant related genes	Relation type
MIR3939	TF binding region
ENSG00000227598	TF binding region
ENSG00000026297	Chromatin interaction
ENSG00000249141	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12193528	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs150116	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs151604	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs162299	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1794698	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs204296	0.85[EUR][1000 genomes]
rs204298	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs375883	0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs388036	0.86[AMR][1000 genomes]
rs414431	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs415356	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs417607	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs425145	0.86[AMR][1000 genomes]
rs435359	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs435688	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs443297	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv605260	chr6:166984094-167455139	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1019381	chr6:167090236-167558598	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv538541	chr6:167090236-167558598	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv948634	chr6:167200671-167838993	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
5	nsv482507	chr6:167282376-167474915	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
6	nsv532074	chr6:167320656-167781977	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
7	nsv1031039	chr6:167324021-167741439	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
8	nsv538543	chr6:167324021-167741439	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
9	nsv1026972	chr6:167335031-167671042	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs239932	AL133458.1	cis	Whole Blood	GTEx
rs239932	CCR6	cis	cerebellum	SCAN
rs239932	RNASET2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:167413600-167414800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
2	chr6:167413600-167414800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
3	chr6:167413600-167415000	Enhancers	Primary B cells from peripheral blood	blood
4	chr6:167413600-167415400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr6:167413600-167415600	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr6:167413600-167419000	Weak transcription	Ovary	ovary
7	chr6:167413600-167419000	Weak transcription	Spleen	Spleen
8	chr6:167413600-167425000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr6:167413600-167425000	Weak transcription	Brain Substantia Nigra	brain
10	chr6:167413600-167425000	Weak transcription	Lung	lung
11	chr6:167413600-167425200	Weak transcription	Esophagus	oesophagus
12	chr6:167413600-167428600	Weak transcription	Aorta	Aorta
13	chr6:167413600-167428800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr6:167413600-167428800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr6:167413600-167438800	Weak transcription	Right Ventricle	heart
16	chr6:167413600-167449200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr6:167413600-167452400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr6:167413800-167414800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr6:167413800-167414800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr6:167413800-167414800	Enhancers	Brain Anterior Caudate	brain
21	chr6:167413800-167414800	Flanking Active TSS	Duodenum Mucosa	Duodenum
22	chr6:167413800-167414800	Enhancers	Fetal Stomach	stomach
23	chr6:167413800-167414800	Enhancers	Placenta Amnion	Placenta Amnion
24	chr6:167413800-167414800	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr6:167413800-167415000	Enhancers	Primary T cells from cord blood	blood
26	chr6:167413800-167415400	Enhancers	Fetal Brain Female	brain
27	chr6:167413800-167415600	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr6:167413800-167417400	Weak transcription	Placenta	Placenta
29	chr6:167413800-167419200	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr6:167413800-167419200	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr6:167413800-167436800	Weak transcription	HSMMtube	muscle
32	chr6:167414000-167415000	Flanking Active TSS	GM12878-XiMat	blood
33	chr6:167414000-167415200	Enhancers	Thymus	Thymus
34	chr6:167414000-167415400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr6:167414000-167415600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr6:167414000-167415800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr6:167414000-167416200	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr6:167414200-167414800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr6:167414200-167414800	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr6:167414200-167414800	Genic enhancers	Fetal Kidney	kidney
41	chr6:167414200-167415000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
42	chr6:167414200-167415200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr6:167414200-167415200	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
44	chr6:167414200-167415200	Enhancers	Gastric	stomach
45	chr6:167414200-167415400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr6:167414200-167415400	Genic enhancers	Fetal Muscle Leg	muscle
47	chr6:167414200-167415400	Genic enhancers	Left Ventricle	heart
48	chr6:167414200-167415400	Enhancers	Pancreas	Pancrea
49	chr6:167414200-167415400	Transcr. at gene 5' and 3'	Dnd41	blood
50	chr6:167414200-167415400	Transcr. at gene 5' and 3'	HepG2	liver

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