Variant report

Variant	rs162295
Chromosome Location	chr6:167454097-167454098
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:167446559..167451164-chr6:167453044..167456262,4	K562	blood:
2	chr6:167453011..167457183-chr6:167458189..167461851,4	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1012656	0.81[CHB][hapmap]
rs1012657	0.81[CHB][hapmap]
rs1079145	0.84[CHD][hapmap];0.82[JPT][hapmap]
rs1331301	0.85[ASN][1000 genomes]
rs1556413	0.81[CHB][hapmap]
rs162287	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs162289	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs162291	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs162293	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs162294	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs162297	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2023305	0.81[CHB][hapmap]
rs2236312	0.84[CHD][hapmap];0.82[JPT][hapmap]
rs239931	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3798307	0.82[JPT][hapmap];0.82[MEX][hapmap]
rs57444856	0.89[ASN][1000 genomes]
rs62436797	0.83[ASN][1000 genomes]
rs7772112	0.85[YRI][hapmap];0.95[ASN][1000 genomes]
rs9366076	0.91[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv464140	chr6:167426681-167492552	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv886943	chr6:167440244-167502638	Strong transcription Flanking Active TSS Genic enhancers Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	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
13	nsv519550	chr6:167450609-167473685	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs162295	RNASET2	cis	cerebellum	SCAN
rs162295	RNASET2	cis	lymphoblastoid	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:167415400-167456600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:167417200-167455400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr6:167417600-167454800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr6:167417800-167455200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr6:167423000-167457600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr6:167437400-167454200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr6:167438000-167456200	Strong transcription	Adipose Nuclei	Adipose
8	chr6:167440400-167459400	Weak transcription	Colon Smooth Muscle	Colon
9	chr6:167441000-167461800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr6:167441200-167454200	Strong transcription	Duodenum Mucosa	Duodenum
11	chr6:167441200-167456600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr6:167441400-167455400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr6:167441400-167456200	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr6:167441400-167473400	Weak transcription	Psoas Muscle	Psoas
15	chr6:167441600-167454200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr6:167441600-167454600	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr6:167441600-167455600	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr6:167441800-167456000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr6:167444800-167456200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr6:167445600-167460200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr6:167447200-167456200	Strong transcription	HepG2	liver
22	chr6:167447400-167455200	Strong transcription	Liver	Liver
23	chr6:167447600-167454200	Strong transcription	Fetal Intestine Large	intestine
24	chr6:167448000-167458400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr6:167448200-167454200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr6:167448200-167456000	Weak transcription	Right Ventricle	heart
27	chr6:167448200-167458200	Weak transcription	Colonic Mucosa	Colon
28	chr6:167448200-167459000	Weak transcription	Rectal Smooth Muscle	rectum
29	chr6:167448200-167459800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr6:167448200-167467200	Weak transcription	HMEC	breast
31	chr6:167448400-167455200	Weak transcription	Brain Angular Gyrus	brain
32	chr6:167448400-167456400	Weak transcription	Hela-S3	cervix
33	chr6:167448400-167467200	Weak transcription	NHEK	skin
34	chr6:167448600-167454600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr6:167448800-167454400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr6:167448800-167460000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr6:167449000-167456000	Weak transcription	Lung	lung
38	chr6:167449000-167456000	Weak transcription	Spleen	Spleen
39	chr6:167449000-167457600	Weak transcription	NHLF	lung
40	chr6:167449000-167458000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr6:167449000-167459400	Weak transcription	Fetal Kidney	kidney
42	chr6:167449000-167467800	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr6:167449000-167470400	Weak transcription	Brain Anterior Caudate	brain
44	chr6:167449200-167454600	Weak transcription	Fetal Heart	heart
45	chr6:167449200-167456000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr6:167449200-167457800	Weak transcription	Pancreas	Pancrea
47	chr6:167449800-167459600	Weak transcription	Brain Cingulate Gyrus	brain
48	chr6:167449800-167462800	Weak transcription	Brain Hippocampus Middle	brain
49	chr6:167450000-167456600	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr6:167450000-167457800	Weak transcription	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links