Variant report

Variant	rs7761485
Chromosome Location	chr6:86113968-86113969
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10944124	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11753050	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11757167	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11759531	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12197281	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1885541	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34201842	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35069263	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6914591	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6919439	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72903444	0.97[ASN][1000 genomes]
rs9689278	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7761485	SNHG5	cis	Muscle Skeletal	GTEx
rs7761485	SNHG5	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86108400-86116600	Enhancers	Fetal Intestine Small	intestine
2	chr6:86110200-86115800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr6:86110200-86116000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr6:86110800-86116600	Enhancers	Fetal Intestine Large	intestine
5	chr6:86111000-86114200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:86111000-86114600	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr6:86111000-86115800	Enhancers	Primary T cells from cord blood	blood
8	chr6:86111000-86116200	Enhancers	Small Intestine	intestine
9	chr6:86111000-86116600	Enhancers	Placenta Amnion	Placenta Amnion
10	chr6:86111200-86114600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr6:86111200-86115200	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr6:86111200-86116200	Enhancers	Stomach Mucosa	stomach
13	chr6:86111200-86116400	Enhancers	Placenta	Placenta
14	chr6:86111400-86114200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr6:86111400-86114200	Enhancers	Colonic Mucosa	Colon
16	chr6:86111400-86115200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr6:86111400-86115600	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr6:86111600-86114000	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr6:86111600-86114400	Weak transcription	Fetal Muscle Leg	muscle
20	chr6:86111600-86115000	Weak transcription	Primary hematopoietic stem cells	blood
21	chr6:86111800-86114200	Enhancers	H9 Cell Line	embryonic stem cell
22	chr6:86111800-86115000	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr6:86112000-86114600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr6:86112000-86114800	Weak transcription	Dnd41	blood
25	chr6:86112200-86114400	Weak transcription	Fetal Thymus	thymus
26	chr6:86112200-86114600	Weak transcription	GM12878-XiMat	blood
27	chr6:86112600-86114400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr6:86112600-86115400	Enhancers	Esophagus	oesophagus
29	chr6:86112800-86114000	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr6:86112800-86114400	Enhancers	Duodenum Mucosa	Duodenum
31	chr6:86112800-86114600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
32	chr6:86112800-86114600	Flanking Active TSS	NH-A	brain
33	chr6:86112800-86114800	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr6:86112800-86115000	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr6:86112800-86115600	Flanking Active TSS	NHEK	skin
36	chr6:86112800-86115800	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr6:86113000-86114000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr6:86113000-86114000	Flanking Active TSS	A549	lung
39	chr6:86113000-86114000	Flanking Active TSS	Hela-S3	cervix
40	chr6:86113000-86114000	Flanking Active TSS	NHDF-Ad	bronchial
41	chr6:86113000-86114200	Flanking Active TSS	HMEC	breast
42	chr6:86113000-86114400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr6:86113000-86114600	Flanking Active TSS	Osteobl	bone
44	chr6:86113000-86115600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr6:86113000-86115600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr6:86113200-86114000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr6:86113200-86114000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr6:86113200-86114000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
49	chr6:86113200-86114200	Weak transcription	Aorta	Aorta
50	chr6:86113200-86114600	Enhancers	iPS-15b Cell Line	embryonic stem cell

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