Variant report

Variant	rs9366078
Chromosome Location	chr6:167399512-167399513
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:167369560..167371875-chr6:167398344..167400077,2	K562	blood:
2	chr6:167389579..167391911-chr6:167397110..167400493,3	K562	blood:

Variant related genes	Relation type
ENSG00000249141	Chromatin interaction
ENSG00000026297	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10946205	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1130033	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]
rs12055488	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13210649	0.87[ASN][1000 genomes]
rs1951459	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs204295	0.83[ASN][1000 genomes]
rs2181059	0.90[ASN][1000 genomes]
rs2237277	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2247314	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2247315	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2247325	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2282860	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2282861	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2285148	0.83[ASN][1000 genomes]
rs2345568	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs239933	0.96[ASN][1000 genomes]
rs2757039	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2757041	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2757053	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs393727	0.83[JPT][hapmap]
rs3963512	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs444210	0.97[ASN][1000 genomes]
rs4710149	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4710154	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4710176	0.82[ASN][1000 genomes]
rs6456143	0.96[ASN][1000 genomes]
rs6907666	0.91[CHB][hapmap]
rs6921588	0.83[ASN][1000 genomes]
rs6936261	0.87[ASN][1000 genomes]
rs6941355	0.80[ASN][1000 genomes]
rs7749278	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7750593	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs933243	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9347170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9355610	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]
rs9356551	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9457258	0.91[ASN][1000 genomes]
rs9459835	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9459842	0.89[ASN][1000 genomes]
rs9459853	0.87[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
rs9366078	RNASET2	cis	Esophagus Mucosa	GTEx
rs9366078	CCR6	cis	cerebellum	SCAN
rs9366078	RNASET2	cis	cerebellum	SCAN
rs9366078	RNASET2	Cis_1M	lymphoblastoid	RTeQTL
rs9366078	CCR6	cis	parietal	SCAN
rs9366078	RNASET2	cis	Whole Blood	GTEx
rs9366078	RNASET2	cis	lymphoblastoid	seeQTL
rs9366078	AL133458.1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:72 , 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	chr6:167381200-167410000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:167381200-167411000	Weak transcription	Fetal Stomach	stomach
5	chr6:167382000-167411200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr6:167382400-167402200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr6:167383200-167411200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:167383400-167411000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr6:167384000-167410600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr6:167384000-167411000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr6:167384000-167411000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr6:167384400-167401400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr6:167384400-167407400	Weak transcription	Fetal Intestine Large	intestine
14	chr6:167384400-167411000	Weak transcription	Fetal Muscle Leg	muscle
15	chr6:167384600-167402800	Weak transcription	Primary B cells from peripheral blood	blood
16	chr6:167384600-167409600	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr6:167385000-167402000	Weak transcription	Fetal Intestine Small	intestine
18	chr6:167385000-167402200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr6:167385000-167411000	Weak transcription	Thymus	Thymus
20	chr6:167385200-167401400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr6:167385400-167401000	Weak transcription	Primary T cells from cord blood	blood
22	chr6:167385400-167402200	Weak transcription	HMEC	breast
23	chr6:167385400-167403000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr6:167385400-167405800	Weak transcription	Primary hematopoietic stem cells	blood
25	chr6:167385400-167411000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr6:167386200-167401600	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr6:167386200-167409400	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr6:167386600-167401600	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr6:167386600-167402000	Weak transcription	NHEK	skin
30	chr6:167386800-167401600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr6:167387600-167402000	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr6:167387800-167401800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr6:167388800-167401400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr6:167388800-167410600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr6:167389600-167411000	Weak transcription	NHLF	lung
36	chr6:167389800-167402400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr6:167390600-167411200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr6:167390800-167411000	Weak transcription	Gastric	stomach
39	chr6:167392200-167399600	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr6:167392200-167411000	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr6:167392400-167402000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr6:167392600-167410800	Weak transcription	HUVEC	blood vessel
43	chr6:167394200-167401400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr6:167394800-167401000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr6:167395000-167401600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr6:167395200-167410200	Weak transcription	Fetal Lung	lung
47	chr6:167396600-167401600	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr6:167396600-167402200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr6:167396800-167401400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr6:167396800-167402800	Weak transcription	Duodenum Mucosa	Duodenum

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