Variant report

Variant	rs2022001
Chromosome Location	chr6:167529509-167529510
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1012656	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[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];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10946211	0.82[ASN][1000 genomes]
rs11967165	0.95[AFR][1000 genomes];0.98[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];0.91[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1556413	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.81[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];0.91[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2021999	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2022000	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2023305	0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3093018	0.81[AMR][1000 genomes]
rs3093026	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55802221	0.81[ASN][1000 genomes]
rs6456157	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456158	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456159	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6908364	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6909252	0.90[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	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6931530	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7749827	0.82[ASN][1000 genomes]
rs9347175	0.91[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	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs968333	0.90[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
rs2022001	RNASET2	cis	Whole Blood	GTEx
rs2022001	CCR6	cis	parietal	SCAN
rs2022001	RNASET2	cis	cerebellum	SCAN
rs2022001	CCR6	cis	cerebellum	SCAN

Chromatin state (count:36 , 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	chr6:167526000-167531600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr6:167526800-167532600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr6:167527000-167532200	Weak transcription	Primary T cells from cord blood	blood
6	chr6:167527200-167529600	Weak transcription	Colonic Mucosa	Colon
7	chr6:167527200-167531800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr6:167527400-167533400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr6:167527600-167531800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr6:167527600-167536200	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr6:167528200-167533600	Weak transcription	Right Atrium	heart
12	chr6:167528400-167529600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:167528600-167531600	Genic enhancers	Primary B cells from peripheral blood	blood
14	chr6:167528600-167532800	Genic enhancers	Primary B cells from cord blood	blood
15	chr6:167528800-167529800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr6:167528800-167529800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
17	chr6:167528800-167530200	Enhancers	Primary T cells fromperipheralblood	blood
18	chr6:167528800-167532200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr6:167529000-167529600	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr6:167529000-167529600	Enhancers	Rectal Smooth Muscle	rectum
21	chr6:167529000-167530000	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr6:167529000-167530600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr6:167529000-167532200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr6:167529200-167531400	Weak transcription	GM12878-XiMat	blood
25	chr6:167529400-167529600	Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr6:167529400-167529600	Enhancers	Adipose Nuclei	Adipose
27	chr6:167529400-167529600	Active TSS	Duodenum Mucosa	Duodenum
28	chr6:167529400-167529800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
29	chr6:167529400-167529800	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr6:167529400-167529800	Enhancers	Esophagus	oesophagus
31	chr6:167529400-167529800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
32	chr6:167529400-167529800	Bivalent Enhancer	HepG2	liver
33	chr6:167529400-167530000	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr6:167529400-167530200	Flanking Active TSS	Colon Smooth Muscle	Colon
35	chr6:167529400-167530200	Flanking Active TSS	Stomach Smooth Muscle	stomach
36	chr6:167529400-167530800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--

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