Variant report

Variant	rs1130033
Chromosome Location	chr6:167385623-167385624
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:167384727..167386679-chr6:167410751..167412327,2	K562	blood:
2	chr6:167383062..167385710-chr6:167390180..167391984,2	MCF-7	breast:
3	chr6:167383885..167385840-chr6:167392702..167394703,2	K562	blood:

Variant related genes	Relation type
ENSG00000265828	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 8 )

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]
rs12055488	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13210649	0.83[ASN][1000 genomes]
rs1951459	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[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	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2247315	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2247325	0.84[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[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs239933	0.92[ASN][1000 genomes]
rs2757039	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2757041	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2757053	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs393727	0.83[JPT][hapmap]
rs3963512	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs444210	0.99[ASN][1000 genomes]
rs4710149	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4710154	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6456143	0.92[ASN][1000 genomes]
rs6907666	0.90[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	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs933243	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9347170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9355610	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]
rs9356551	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9366078	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[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:9 , 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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1130033	CCR6	cis	cerebellum	SCAN
rs1130033	RNASET2	cis	lymphoblastoid	seeQTL
rs1130033	RNASET2	cis	cerebellum	SCAN
rs1130033	RNASET2	cis	Esophagus Mucosa	GTEx
rs1130033	RNASET2	Cis_1M	lymphoblastoid	RTeQTL
rs1130033	RNASET2	cis	Whole Blood	GTEx
rs1130033	CCR6	cis	parietal	SCAN
rs1130033	AL133458.1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:54 , 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	chr6:167378800-167398600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr6:167380800-167391000	Weak transcription	Osteobl	bone
5	chr6:167381200-167410000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:167381200-167411000	Weak transcription	Fetal Stomach	stomach
7	chr6:167381800-167391200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr6:167381800-167396200	Weak transcription	HepG2	liver
9	chr6:167382000-167411200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr6:167382400-167392400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr6:167382400-167402200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr6:167382600-167392000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:167383200-167396200	Weak transcription	Fetal Brain Female	brain
14	chr6:167383200-167411200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr6:167383400-167386200	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr6:167383400-167386600	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr6:167383400-167387200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr6:167383400-167389800	Weak transcription	K562	blood
19	chr6:167383400-167411000	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr6:167383600-167391000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr6:167383800-167385800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr6:167383800-167392000	Weak transcription	Brain Germinal Matrix	brain
23	chr6:167384000-167396200	Weak transcription	GM12878-XiMat	blood
24	chr6:167384000-167410600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr6:167384000-167411000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr6:167384000-167411000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr6:167384400-167385800	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr6:167384400-167386200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
29	chr6:167384400-167401400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr6:167384400-167407400	Weak transcription	Fetal Intestine Large	intestine
31	chr6:167384400-167411000	Weak transcription	Fetal Muscle Leg	muscle
32	chr6:167384600-167386800	Genic enhancers	Dnd41	blood
33	chr6:167384600-167396200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr6:167384600-167398600	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr6:167384600-167402800	Weak transcription	Primary B cells from peripheral blood	blood
36	chr6:167384600-167409600	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr6:167384800-167386200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
38	chr6:167384800-167399200	Weak transcription	Primary B cells from cord blood	blood
39	chr6:167385000-167386000	Genic enhancers	Fetal Thymus	thymus
40	chr6:167385000-167387800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr6:167385000-167402000	Weak transcription	Fetal Intestine Small	intestine
42	chr6:167385000-167402200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr6:167385000-167411000	Weak transcription	Thymus	Thymus
44	chr6:167385200-167385800	Genic enhancers	Primary neutrophils fromperipheralblood	blood
45	chr6:167385200-167389800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr6:167385200-167401400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr6:167385400-167386800	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr6:167385400-167401000	Weak transcription	Primary T cells from cord blood	blood
49	chr6:167385400-167402200	Weak transcription	HMEC	breast
50	chr6:167385400-167403000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links