Variant report

Variant	rs9459874
Chromosome Location	chr6:167504127-167504128
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 101 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10484530	0.80[AMR][1000 genomes]
rs10946208	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12178491	0.80[AMR][1000 genomes]
rs12203510	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12209395	0.82[AMR][1000 genomes]
rs12213683	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12523712	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12526548	0.95[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs12527827	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12528323	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12528689	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12529238	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12529876	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12529959	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13204839	0.84[AMR][1000 genomes]
rs13208636	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13210649	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13213249	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1358882	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1358883	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1407315	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17524252	0.84[AMR][1000 genomes]
rs17615336	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1810644	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1810645	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1894603	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[ASN][1000 genomes]
rs2001114	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2001115	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2017338	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2181058	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2236313	0.80[JPT][hapmap]
rs2237273	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2237274	0.83[JPT][hapmap]
rs2239823	0.80[AMR][1000 genomes]
rs2239826	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2239827	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2285147	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2285148	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2301436	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs35171809	0.87[ASN][1000 genomes]
rs4710175	0.84[AMR][1000 genomes]
rs4710176	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4710185	0.87[MEX][hapmap]
rs62436765	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6456146	0.87[ASN][1000 genomes]
rs6456149	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6456150	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6456151	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6456152	0.84[AMR][1000 genomes]
rs6456153	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6456154	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6902119	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6909180	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6909475	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6909502	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6918286	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6920858	0.84[AMR][1000 genomes]
rs6921588	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6932740	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6934043	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6936261	0.87[EUR][1000 genomes]
rs6941355	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs720325	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7742305	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7748224	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7760495	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7761977	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7762156	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7766242	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs911632	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs916331	0.84[AMR][1000 genomes]
rs9295384	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9457249	0.83[JPT][hapmap]
rs9457257	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9457260	0.84[AMR][1000 genomes]
rs9457261	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9457268	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9457270	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9459839	0.87[ASN][1000 genomes]
rs9459845	0.87[ASN][1000 genomes]
rs9459846	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9459853	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9459854	0.84[AMR][1000 genomes]
rs9459855	0.84[AMR][1000 genomes]
rs9459862	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9459871	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9459872	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs9459874	CCR6	cis	parietal	SCAN
rs9459874	TCTE3	cis	parietal	SCAN
rs9459874	CCR6	cis	multi-tissue	Pritchard
rs9459874	RNASET2	cis	Whole Blood	GTEx
rs9459874	RNASET2	cis	cerebellum	SCAN
rs9459874	AL133458.1	cis	Whole Blood	GTEx
rs9459874	AL133458.1	cis	lung	GTEx
rs9459874	CCR6	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:167502000-167506000	Enhancers	Primary B cells from peripheral blood	blood
2	chr6:167502200-167504600	Enhancers	Primary B cells from cord blood	blood
3	chr6:167502800-167506200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr6:167502800-167507400	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr6:167503000-167504200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr6:167503000-167504200	Enhancers	Adipose Nuclei	Adipose
7	chr6:167503000-167504400	Enhancers	Fetal Muscle Leg	muscle
8	chr6:167503000-167506200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr6:167503200-167504200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr6:167503200-167504200	Enhancers	Placenta	Placenta
11	chr6:167503200-167505600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr6:167503200-167508000	Weak transcription	Gastric	stomach
13	chr6:167503200-167509800	Enhancers	Primary hematopoietic stem cells	blood
14	chr6:167503400-167504400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr6:167503400-167506200	Enhancers	Thymus	Thymus
16	chr6:167503600-167504600	Weak transcription	Spleen	Spleen
17	chr6:167503600-167505200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr6:167503600-167506400	Enhancers	Primary T cells fromperipheralblood	blood
19	chr6:167503600-167506400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr6:167503600-167507200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr6:167503600-167507600	Weak transcription	Right Atrium	heart
22	chr6:167503600-167527200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr6:167503800-167504800	Flanking Active TSS	GM12878-XiMat	blood
24	chr6:167503800-167506000	Enhancers	Fetal Thymus	thymus
25	chr6:167503800-167506400	Enhancers	Primary T cells from cord blood	blood
26	chr6:167503800-167506600	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr6:167503800-167507400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr6:167504000-167504200	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr6:167504000-167505200	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr6:167504000-167506200	Enhancers	Primary hematopoietic stem cells short term culture	blood

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