Variant report

Variant	rs313201
Chromosome Location	chr6:86111201-86111202
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs188752	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs313193	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs313194	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs313196	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs313198	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs313199	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4326211	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs528426	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs532366	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs545407	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs547037	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs550763	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs560334	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs577388	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs597623	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs600610	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs614124	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs615848	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs626741	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs634511	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs645265	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs645354	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs659755	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs688839	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs692830	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7775853	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017418	chr6:85344786-86259540	Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv538347	chr6:85344786-86259540	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1022445	chr6:85972678-86392968	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
4	nsv538349	chr6:85972678-86392968	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
5	nsv830721	chr6:85987644-86147414	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv3326486	chr6:86020165-86292456	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv1019960	chr6:86023236-86136666	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv3435075	chr6:86052235-86271910	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs313201	SNHG5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86101000-86111400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:86105800-86111400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr6:86106200-86111600	Weak transcription	Liver	Liver
4	chr6:86108000-86111400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr6:86108400-86116600	Enhancers	Fetal Intestine Small	intestine
6	chr6:86108800-86113400	Enhancers	HepG2	liver
7	chr6:86109400-86112000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:86109400-86113000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr6:86109600-86113000	Weak transcription	Pancreas	Pancrea
10	chr6:86109800-86111400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:86110000-86112800	Enhancers	Muscle Satellite Cultured Cells	--
12	chr6:86110000-86113000	Enhancers	HUVEC	blood vessel
13	chr6:86110200-86115800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr6:86110200-86116000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr6:86110400-86113000	Enhancers	A549	lung
16	chr6:86110400-86113000	Enhancers	Osteobl	bone
17	chr6:86110800-86116600	Enhancers	Fetal Intestine Large	intestine
18	chr6:86111000-86111400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr6:86111000-86111400	Enhancers	Fetal Lung	lung
20	chr6:86111000-86111600	Enhancers	Primary hematopoietic stem cells	blood
21	chr6:86111000-86111800	Enhancers	Pancreatic Islets	Pancreatic Islet
22	chr6:86111000-86112200	Enhancers	Fetal Thymus	thymus
23	chr6:86111000-86112200	Enhancers	GM12878-XiMat	blood
24	chr6:86111000-86112400	Enhancers	Duodenum Mucosa	Duodenum
25	chr6:86111000-86112600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr6:86111000-86112800	Enhancers	NH-A	brain
27	chr6:86111000-86113000	Enhancers	Hela-S3	cervix
28	chr6:86111000-86113200	Enhancers	Rectal Mucosa Donor 29	rectum
29	chr6:86111000-86113200	Enhancers	NHLF	lung
30	chr6:86111000-86113600	Enhancers	Adipose Nuclei	Adipose
31	chr6:86111000-86113800	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr6:86111000-86114200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr6:86111000-86114600	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr6:86111000-86115800	Enhancers	Primary T cells from cord blood	blood
35	chr6:86111000-86116200	Enhancers	Small Intestine	intestine
36	chr6:86111000-86116600	Enhancers	Placenta Amnion	Placenta Amnion
37	chr6:86111200-86111400	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr6:86111200-86111600	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr6:86111200-86111600	Enhancers	Primary B cells from cord blood	blood
40	chr6:86111200-86111600	Enhancers	Fetal Muscle Leg	muscle
41	chr6:86111200-86111600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
42	chr6:86111200-86112800	Enhancers	NHEK	skin
43	chr6:86111200-86113000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr6:86111200-86113000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr6:86111200-86113000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr6:86111200-86113000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr6:86111200-86113000	Enhancers	HMEC	breast
48	chr6:86111200-86113000	Enhancers	NHDF-Ad	bronchial
49	chr6:86111200-86113200	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr6:86111200-86113200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links