Variant report

Variant	rs7746065
Chromosome Location	chr6:86174845-86174846
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:86168171..86170047-chr6:86172335..86175305,2	MCF-7	breast:
2	chr6:86159467..86161013-chr6:86173619..86175929,2	K562	blood:

Variant related genes	Relation type
ENSG00000135318	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs12199873	0.91[CHB][hapmap]
rs1590281	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2065114	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2208725	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2229523	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2475790	0.91[CHB][hapmap]
rs2475791	0.91[CHB][hapmap]
rs2758840	0.91[CHB][hapmap]
rs2758846	0.91[CHB][hapmap]
rs2758847	0.91[CHB][hapmap]
rs2842601	0.86[CHB][hapmap]
rs2842604	0.91[CHB][hapmap]
rs2842607	0.91[CHB][hapmap]
rs2842608	0.91[CHB][hapmap]
rs2842612	0.91[CHB][hapmap]
rs2842613	0.91[CHB][hapmap]
rs3812133	0.86[CHB][hapmap]
rs4235826	0.90[CEU][hapmap];0.91[CHB][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4235827	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4282381	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4304137	0.87[CHB][hapmap];0.81[ASN][1000 genomes]
rs4351223	0.91[CHB][hapmap]
rs4373337	0.91[CEU][hapmap]
rs4419647	0.81[ASN][1000 genomes]
rs4441928	0.91[CHB][hapmap]
rs4501401	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4562107	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4579322	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4593336	0.91[CEU][hapmap]
rs4707207	0.90[CEU][hapmap];0.95[CHB][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6454468	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6454469	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6454471	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs6922	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs6931295	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7452605	0.91[CHB][hapmap]
rs7739563	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7765636	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7770359	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9294337	0.91[CHB][hapmap]
rs9344532	0.91[CHB][hapmap]
rs9351065	0.91[CHB][hapmap]
rs9353318	0.91[CHB][hapmap]
rs9362230	0.91[CHB][hapmap]
rs9444349	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9450272	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9450282	0.81[CEU][hapmap]

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	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	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
6	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
7	nsv463937	chr6:86114766-86264374	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv604092	chr6:86114766-86264374	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv520112	chr6:86144875-86247759	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs7746065	SNHG5	cis	Thyroid	GTEx
rs7746065	SNHG5	cis	Whole Blood	GTEx
rs7746065	SNHG5	cis	Esophagus Mucosa	GTEx
rs7746065	C6orf160	cis	lesional skin	skin_eQTL
rs7746065	SNHG5	cis	Artery Tibial	GTEx
rs7746065	SNHG5	cis	lung	GTEx
rs7746065	SNHG5	cis	Muscle Skeletal	GTEx
rs7746065	C6orf160	cis	normal skin	skin_eQTL
rs7746065	SNHG5	cis	multi-tissue	Pritchard
rs7746065	SNHG5	cis	Adipose Subcutaneous	GTEx
rs7746065	SNHG5	cis	Skin Sun Exposed Lower leg	GTEx
rs7746065	SNHG5	Cis_1M	lymphoblastoid	RTeQTL
rs7746065	NT5E	Cis_1M	lymphoblastoid	RTeQTL
rs7746065	C6orf160	cis	uninvolved skin	skin_eQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86163200-86176600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
2	chr6:86167800-86176200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:86171800-86176800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr6:86171800-86185200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr6:86171800-86186000	Weak transcription	Fetal Stomach	stomach
6	chr6:86171800-86187600	Weak transcription	Colonic Mucosa	Colon
7	chr6:86172000-86179000	Weak transcription	Pancreas	Pancrea
8	chr6:86172200-86179800	Weak transcription	Left Ventricle	heart
9	chr6:86172200-86186000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr6:86172400-86175400	Weak transcription	Lung	lung
11	chr6:86172400-86176200	Enhancers	Primary T cells from cord blood	blood
12	chr6:86172400-86178000	Weak transcription	Aorta	Aorta
13	chr6:86172400-86192800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr6:86172600-86175400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr6:86173200-86176200	Enhancers	GM12878-XiMat	blood
16	chr6:86173400-86175000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr6:86173400-86175000	Flanking Active TSS	A549	lung
18	chr6:86173400-86175600	Enhancers	Primary hematopoietic stem cells	blood
19	chr6:86173400-86176000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:86173600-86175600	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr6:86173800-86175000	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr6:86173800-86175000	Flanking Active TSS	Hela-S3	cervix
23	chr6:86174000-86175000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr6:86174000-86175000	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
25	chr6:86174000-86175200	Enhancers	Fetal Thymus	thymus
26	chr6:86174000-86175600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr6:86174000-86175800	Enhancers	Spleen	Spleen
28	chr6:86174000-86176600	Enhancers	Placenta	Placenta
29	chr6:86174200-86175000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr6:86174200-86175000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:86174200-86175000	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr6:86174200-86175000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr6:86174200-86175000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
34	chr6:86174200-86175000	Flanking Active TSS	HSMMtube	muscle
35	chr6:86174200-86175200	Flanking Active TSS	HUVEC	blood vessel
36	chr6:86174200-86175400	Flanking Active TSS	NH-A	brain
37	chr6:86174200-86175600	Enhancers	Colon Smooth Muscle	Colon
38	chr6:86174200-86175600	Enhancers	Ovary	ovary
39	chr6:86174200-86175600	Enhancers	Stomach Smooth Muscle	stomach
40	chr6:86174200-86175800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr6:86174200-86176000	Enhancers	Esophagus	oesophagus
42	chr6:86174200-86176200	Weak transcription	Liver	Liver
43	chr6:86174200-86177000	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr6:86174400-86175000	Transcr. at gene 5' and 3'	HSMM	muscle
45	chr6:86174400-86175400	Weak transcription	Primary B cells from peripheral blood	blood
46	chr6:86174400-86176000	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr6:86174400-86176000	Weak transcription	Gastric	stomach
48	chr6:86174400-86176200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr6:86174400-86176200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr6:86174600-86175000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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