Variant report

Variant	rs9355610
Chromosome Location	chr6:167383075-167383076
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:167382648..167385296-chr6:167441304..167444220,2	K562	blood:
2	chr6:167368947..167371010-chr6:167382080..167384318,2	K562	blood:
3	chr6:167383062..167385710-chr6:167390180..167391984,2	MCF-7	breast:
4	chr6:167368947..167370452-chr6:167382818..167385059,2	K562	blood:

Variant related genes	Relation type
ENSG00000249141	Chromatin interaction
ENSG00000026297	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs10946205	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1130033	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12055488	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13210649	0.83[ASN][1000 genomes]
rs1951459	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2181059	0.86[ASN][1000 genomes]
rs2237277	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2247314	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2247315	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2247325	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2282860	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2282861	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2345568	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs239933	0.92[ASN][1000 genomes]
rs2757039	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2757041	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2757053	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs393727	0.83[JPT][hapmap]
rs3963512	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs444210	0.99[ASN][1000 genomes]
rs4710149	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4710154	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6456143	0.92[ASN][1000 genomes]
rs6907666	0.91[CHB][hapmap]
rs6936261	0.83[ASN][1000 genomes]
rs7749278	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7750593	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs933243	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9347170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9356551	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9366078	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9457258	0.87[ASN][1000 genomes]
rs9459835	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9459842	0.85[ASN][1000 genomes]
rs9459853	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv605260	chr6:166984094-167455139	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	nsv482507	chr6:167282376-167474915	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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
10	nsv1034359	chr6:167359643-167384714	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Graves' disease	21841780	GWAS catalog

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs9355610	RNASET2	Cis_1M	lymphoblastoid	RTeQTL
rs9355610	RNASET2	cis	Whole Blood	GTEx
rs9355610	RNASET2	cis	cerebellum	SCAN
rs9355610	CCR6	cis	cerebellum	SCAN
rs9355610	AL133458.1	cis	Skin Sun Exposed Lower leg	GTEx
rs9355610	RNASET2	cis	lymphoblastoid	seeQTL
rs9355610	CCR6	cis	parietal	SCAN
rs9355610	RNASET2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:167371400-167411000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:167373600-167402400	Weak transcription	Liver	Liver
3	chr6:167373800-167384800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:167378800-167398600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr6:167380600-167384200	Weak transcription	Fetal Intestine Small	intestine
6	chr6:167380800-167383800	Weak transcription	Placenta	Placenta
7	chr6:167380800-167391000	Weak transcription	Osteobl	bone
8	chr6:167381200-167384200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr6:167381200-167410000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:167381200-167411000	Weak transcription	Fetal Stomach	stomach
11	chr6:167381600-167385200	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr6:167381800-167391200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr6:167381800-167396200	Weak transcription	HepG2	liver
14	chr6:167382000-167411200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr6:167382200-167385400	Enhancers	Primary T cells fromperipheralblood	blood
16	chr6:167382400-167384400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr6:167382400-167392400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr6:167382400-167402200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr6:167382600-167383600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr6:167382600-167383600	Flanking Active TSS	Primary T cells from cord blood	blood
21	chr6:167382600-167384400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr6:167382600-167384400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr6:167382600-167384800	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr6:167382600-167385200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr6:167382600-167385400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr6:167382600-167392000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr6:167382800-167383200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
28	chr6:167382800-167383200	Enhancers	Brain Anterior Caudate	brain
29	chr6:167382800-167383200	Flanking Active TSS	Dnd41	blood
30	chr6:167382800-167383400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
31	chr6:167382800-167383400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr6:167382800-167383400	ZNF genes & repeats	K562	blood
33	chr6:167382800-167383800	Enhancers	NHDF-Ad	bronchial
34	chr6:167382800-167384000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
35	chr6:167382800-167384400	Enhancers	Monocytes-CD14+_RO01746	blood
36	chr6:167382800-167384600	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr6:167382800-167384600	Enhancers	Primary B cells from peripheral blood	blood
38	chr6:167382800-167385000	Enhancers	Fetal Thymus	thymus
39	chr6:167383000-167383200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
40	chr6:167383000-167383200	Enhancers	Fetal Brain Female	brain
41	chr6:167383000-167383400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
42	chr6:167383000-167383400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr6:167383000-167383400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr6:167383000-167383600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr6:167383000-167383800	Flanking Active TSS	Primary B cells from cord blood	blood
46	chr6:167383000-167383800	Flanking Active TSS	Primary hematopoietic stem cells	blood
47	chr6:167383000-167383800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr6:167383000-167384000	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr6:167383000-167384000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr6:167383000-167384000	Enhancers	GM12878-XiMat	blood

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