Variant report

Variant	rs10946213
Chromosome Location	chr6:167516095-167516096
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:167514455..167516810-chr6:167518589..167520872,3	K562	blood:
2	chr6:167514528..167517115-chr6:167518866..167520880,2	MCF-7	breast:
3	chr6:167515250..167516810-chr6:167519372..167521331,2	K562	blood:

Extended variants
information (count: 49 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10946211	0.90[EUR][1000 genomes]
rs10946212	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10946214	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10946215	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10946216	0.85[JPT][hapmap]
rs12178491	0.87[AMR][1000 genomes]
rs12193698	0.84[AMR][1000 genomes]
rs150108	0.81[EUR][1000 genomes]
rs150112	0.90[EUR][1000 genomes]
rs1571878	0.85[JPT][hapmap]
rs2021033	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2039321	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs204293	0.90[EUR][1000 genomes]
rs2239823	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4709148	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4710178	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4710179	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4710181	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4710182	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4710183	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55802221	0.98[EUR][1000 genomes]
rs6456156	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6905876	0.82[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.82[TSI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6905911	0.82[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.82[TSI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7749827	0.90[EUR][1000 genomes]
rs7761159	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7765739	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7774396	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7775443	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9364891	0.90[EUR][1000 genomes]
rs9366089	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9457270	0.85[AMR][1000 genomes]
rs9457273	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9457274	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs975822	0.90[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10946213	RNASET2	cis	cerebellum	SCAN
rs10946213	CCR6	cis	cerebellum	SCAN
rs10946213	RNASET2	cis	Whole Blood	GTEx
rs10946213	AL133458.1	cis	Whole Blood	GTEx
rs10946213	CCR6	cis	multi-tissue	Pritchard
rs10946213	CCR6	cis	parietal	SCAN

Chromatin state (count:28 , 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	chr6:167509000-167516400	Enhancers	Primary B cells from cord blood	blood
3	chr6:167509000-167525200	Enhancers	Primary B cells from peripheral blood	blood
4	chr6:167509800-167516200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr6:167510000-167516600	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr6:167511200-167517400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr6:167512600-167518800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:167512800-167516600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr6:167512800-167516600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr6:167512800-167518000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr6:167512800-167518400	Weak transcription	Thymus	Thymus
12	chr6:167513000-167516400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr6:167513200-167516200	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr6:167513200-167516400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr6:167513200-167516400	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr6:167513200-167516400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr6:167513400-167516200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr6:167513400-167516400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr6:167513600-167516400	Weak transcription	Fetal Thymus	thymus
20	chr6:167514600-167516400	Weak transcription	Ovary	ovary
21	chr6:167515000-167516400	Weak transcription	Fetal Intestine Large	intestine
22	chr6:167515600-167518000	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr6:167515800-167516400	Enhancers	GM12878-XiMat	blood
24	chr6:167515800-167516400	Bivalent Enhancer	HepG2	liver
25	chr6:167515800-167517600	Enhancers	Spleen	Spleen
26	chr6:167515800-167518200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr6:167516000-167516600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr6:167516000-167517400	Enhancers	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links