Variant report

Variant	rs6456158
Chromosome Location	chr6:167528032-167528033
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1012656	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1012657	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10946211	0.82[ASN][1000 genomes]
rs11967165	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1331299	1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1556413	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[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	0.83[CHB][hapmap]
rs1854853	0.81[TSI][hapmap]
rs1855025	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2021999	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2022000	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2022001	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2023305	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3093026	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55802221	0.81[ASN][1000 genomes]
rs6456157	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456159	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6908364	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6909252	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6911766	0.81[ASN][1000 genomes]
rs6916486	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6930998	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6931530	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7749827	0.82[ASN][1000 genomes]
rs9347175	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9364891	0.82[ASN][1000 genomes]
rs9366076	0.81[CHB][hapmap]
rs9459882	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs968333	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs975822	0.82[ASN][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6456158	CCR6	cis	cerebellum	SCAN
rs6456158	RNASET2	cis	cerebellum	SCAN
rs6456158	CCR6	cis	multi-tissue	Pritchard
rs6456158	CCR6	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:167517600-167529800	Weak transcription	Spleen	Spleen
2	chr6:167520400-167529800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:167525000-167529000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
4	chr6:167525200-167528600	Flanking Active TSS	Primary B cells from peripheral blood	blood
5	chr6:167525800-167528400	Flanking Active TSS	GM12878-XiMat	blood
6	chr6:167526000-167531600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr6:167526600-167528800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
8	chr6:167526800-167529000	Enhancers	Placenta Amnion	Placenta Amnion
9	chr6:167526800-167532600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr6:167527000-167529000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr6:167527000-167532200	Weak transcription	Primary T cells from cord blood	blood
12	chr6:167527200-167529600	Weak transcription	Colonic Mucosa	Colon
13	chr6:167527200-167531800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr6:167527400-167528200	Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr6:167527400-167528400	Bivalent Enhancer	Fetal Muscle Leg	muscle
16	chr6:167527400-167528800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr6:167527400-167533400	Weak transcription	Primary hematopoietic stem cells	blood
18	chr6:167527600-167528600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr6:167527600-167531800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr6:167527600-167536200	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr6:167527800-167528200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr6:167527800-167528800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
23	chr6:167527800-167529200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
24	chr6:167527800-167529400	Weak transcription	Duodenum Mucosa	Duodenum
25	chr6:167527800-167529400	Weak transcription	Esophagus	oesophagus
26	chr6:167528000-167528200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
27	chr6:167528000-167528200	Bivalent Enhancer	Fetal Stomach	stomach
28	chr6:167528000-167528200	Enhancers	Right Atrium	heart
29	chr6:167528000-167528600	Flanking Active TSS	Primary B cells from cord blood	blood

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