Variant report

Variant	rs1331299
Chromosome Location	chr6:167533467-167533468
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	TBL1XR1	chr6:167533434-167533737	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:167531624-167537352	GM12891	blood:	n/a	n/a
3	POLR2A	chr6:167533275-167536808	GM12892	blood:	n/a	n/a
4	RELA	chr6:167533130-167533934	GM19099	blood:	n/a	n/a
5	TRIM28	chr6:167533463-167533974	K562	blood:	n/a	n/a
6	MTA3	chr6:167533146-167534481	GM12878	blood:	n/a	n/a
7	RUNX3	chr6:167533109-167533973	GM12878	blood:	n/a	n/a
8	TCF3	chr6:167533218-167533478	GM12878	blood:	n/a	chr6:167533408-167533417
9	KAP1	chr6:167533417-167534036	K562	blood:	n/a	n/a
10	RELA	chr6:167533233-167534192	GM12891	blood:	n/a	n/a
11	TCF3	chr6:167533285-167533484	GM12878	blood:	n/a	chr6:167533408-167533417
12	RUNX3	chr6:167533121-167533878	GM12878	blood:	n/a	n/a
13	POLR2A	chr6:167533281-167537302	GM12878	blood:	n/a	n/a
14	RELA	chr6:167533266-167534174	GM18951	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:167533318..167534107-chr6:167555281..167555885,2	MCF-7	breast:

Variant related genes	Relation type
CCR6	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1012656	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1012657	1.00[CEU][hapmap];0.85[JPT][hapmap];0.96[EUR][1000 genomes]
rs11967165	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1556413	1.00[CEU][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs1854853	0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1855025	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2021999	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2022000	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2022001	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2023305	0.85[CEU][hapmap];0.82[CHB][hapmap];0.81[GIH][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs3093018	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3093019	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3093026	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6456157	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6456158	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6456159	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6908364	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6909252	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6916486	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6930998	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6931530	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9347175	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9459882	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs968333	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	esv2752099	chr6:167448181-167579102	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1018193	chr6:167491589-167797294	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv538544	chr6:167491589-167797294	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv469673	chr6:167500376-167658532	Flanking Active TSS Genic enhancers Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	nsv482439	chr6:167500376-167658532	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	esv2758094	chr6:167501204-167845935	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
14	esv2759492	chr6:167501204-168176733	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
15	nsv482873	chr6:167521620-167679133	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	nsv1024657	chr6:167526198-167555488	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1331299	AL133458.1	cis	Whole Blood	GTEx
rs1331299	CCR6	cis	multi-tissue	Pritchard
rs1331299	RNASET2	cis	cerebellum	SCAN
rs1331299	PTPRK	trans	lymphoblastoid	seeQTL
rs1331299	CCR6	cis	parietal	SCAN
rs1331299	RNASET2	cis	Whole Blood	GTEx
rs1331299	CCR6	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:167527600-167536200	Enhancers	Primary T helper cells fromperipheralblood	blood
2	chr6:167528200-167533600	Weak transcription	Right Atrium	heart
3	chr6:167530200-167533600	Weak transcription	Ovary	ovary
4	chr6:167530200-167535200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr6:167530200-167543200	Weak transcription	Spleen	Spleen
6	chr6:167530400-167538200	Weak transcription	Gastric	stomach
7	chr6:167530600-167533600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr6:167530800-167542800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr6:167531400-167536400	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr6:167531600-167534400	Flanking Active TSS	GM12878-XiMat	blood
11	chr6:167531800-167533600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
12	chr6:167532000-167535800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr6:167532200-167534400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr6:167532200-167535600	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr6:167532200-167536000	Enhancers	Primary T cells from cord blood	blood
16	chr6:167532400-167534000	Enhancers	Fetal Thymus	thymus
17	chr6:167532400-167535000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr6:167532600-167533800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr6:167532600-167534200	Enhancers	Thymus	Thymus
20	chr6:167532600-167536000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr6:167532800-167534000	Flanking Active TSS	Primary B cells from cord blood	blood
22	chr6:167532800-167534000	Weak transcription	Duodenum Mucosa	Duodenum
23	chr6:167532800-167536400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr6:167532800-167536600	Weak transcription	Colonic Mucosa	Colon
25	chr6:167533000-167533600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr6:167533000-167535600	Enhancers	Primary T cells fromperipheralblood	blood
27	chr6:167533200-167534000	Enhancers	Rectal Smooth Muscle	rectum
28	chr6:167533200-167534200	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr6:167533200-167534200	ZNF genes & repeats	HepG2	liver
30	chr6:167533200-167535400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr6:167533200-167536400	Enhancers	Fetal Intestine Large	intestine
32	chr6:167533200-167536400	Enhancers	Fetal Intestine Small	intestine
33	chr6:167533400-167533600	Enhancers	Primary hematopoietic stem cells	blood
34	chr6:167533400-167533800	Enhancers	Primary B cells from peripheral blood	blood
35	chr6:167533400-167534000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
36	chr6:167533400-167534400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr6:167533400-167535200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr6:167533400-167535800	Weak transcription	Stomach Mucosa	stomach
39	chr6:167533400-167536600	Enhancers	Primary hematopoietic stem cells short term culture	blood

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