Variant report

Variant	rs1855025
Chromosome Location	chr6:167537594-167537595
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1012656	1.00[CEU][hapmap];0.81[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];0.80[ASN][1000 genomes]
rs1331299	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]
rs1556413	1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs1854853	0.83[GIH][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2021999	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][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];0.81[CHB][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs3093018	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3093019	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3093026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[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:17 , 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
17	esv3389542	chr6:167536262-167540560	Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1855025	RNASET2	cis	cerebellum	SCAN
rs1855025	CCR6	cis	parietal	SCAN
rs1855025	CCR6	cis	cerebellum	SCAN
rs1855025	RNASET2	cis	Whole Blood	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:167530200-167543200	Weak transcription	Spleen	Spleen
2	chr6:167530400-167538200	Weak transcription	Gastric	stomach
3	chr6:167530800-167542800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:167534000-167573400	Weak transcription	Right Atrium	heart
5	chr6:167534400-167537800	Flanking Active TSS	Primary B cells from cord blood	blood
6	chr6:167534800-167538800	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr6:167534800-167539000	Flanking Active TSS	GM12878-XiMat	blood
8	chr6:167535200-167537600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
9	chr6:167535600-167554000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr6:167536000-167538000	Flanking Active TSS	HepG2	liver
11	chr6:167536200-167538600	Active TSS	Rectal Smooth Muscle	rectum
12	chr6:167536200-167539200	Active TSS	Rectal Mucosa Donor 29	rectum
13	chr6:167536200-167539800	Enhancers	Primary hematopoietic stem cells	blood
14	chr6:167536400-167539200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr6:167536400-167539200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr6:167536600-167537600	Active TSS	Colonic Mucosa	Colon
17	chr6:167536600-167538600	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr6:167537000-167538200	Weak transcription	Stomach Mucosa	stomach
19	chr6:167537000-167538400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr6:167537000-167539200	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr6:167537000-167539200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr6:167537000-167540400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr6:167537000-167546000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr6:167537200-167537600	Enhancers	Primary T cells fromperipheralblood	blood
25	chr6:167537200-167537600	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr6:167537200-167538000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr6:167537200-167538000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr6:167537200-167539000	Active TSS	Primary B cells from peripheral blood	blood
29	chr6:167537200-167543000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr6:167537400-167537600	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr6:167537400-167537600	Enhancers	Fetal Intestine Large	intestine
32	chr6:167537400-167538200	Weak transcription	Duodenum Mucosa	Duodenum
33	chr6:167537400-167541000	Weak transcription	Fetal Intestine Small	intestine

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