Variant report

Variant	rs1556413
Chromosome Location	chr6:167524743-167524744
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	chr6:167524690-167524953	K562	blood:	n/a	chr6:167524829-167524838 chr6:167524771-167524780

Variant related genes	Relation type
CCR6	TF binding region

Extended variants
information (count: 54 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1012656	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1012657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10946211	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11967165	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1331299	1.00[CEU][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs150108	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs150110	0.90[ASN][1000 genomes]
rs162289	0.86[CHB][hapmap]
rs162291	0.86[CHB][hapmap]
rs162293	0.86[CHB][hapmap]
rs162294	0.86[CHB][hapmap]
rs162295	0.81[CHB][hapmap]
rs162297	0.82[CHB][hapmap]
rs1854853	0.81[GIH][hapmap]
rs1855025	1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs2021033	0.85[AMR][1000 genomes]
rs2021999	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2022000	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2022001	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2023305	0.91[ASW][hapmap];0.85[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs204293	0.84[AMR][1000 genomes]
rs3093026	1.00[CEU][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs55802221	0.93[ASN][1000 genomes]
rs6456157	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6456158	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6456159	0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6908364	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6909252	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6911766	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6916486	0.95[EUR][1000 genomes]
rs6930998	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6931530	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7749827	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9347175	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9364891	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9366076	0.82[CHB][hapmap]
rs9459882	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs968333	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs975822	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1556413	CCR6	cis	cerebellum	SCAN
rs1556413	RNASET2	cis	cerebellum	SCAN
rs1556413	CCR6	cis	parietal	SCAN
rs1556413	RNASET2	cis	Whole Blood	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:167503600-167527200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:167509000-167525200	Enhancers	Primary B cells from peripheral blood	blood
3	chr6:167517600-167529800	Weak transcription	Spleen	Spleen
4	chr6:167519400-167527800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:167520400-167529800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:167523600-167525000	Enhancers	GM12878-XiMat	blood
7	chr6:167523800-167524800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
8	chr6:167524000-167524800	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr6:167524000-167524800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr6:167524000-167525000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr6:167524000-167525200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr6:167524200-167525000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
13	chr6:167524200-167525200	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr6:167524200-167526800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr6:167524400-167527400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr6:167524600-167525000	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr6:167524600-167525200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr6:167524600-167525400	Flanking Active TSS	Primary B cells from cord blood	blood

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