Variant report

Variant	rs4373337
Chromosome Location	chr6:86179406-86179407
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr6:86178795-86179515	HCT-116	colon:	n/a	n/a
2	FOSL1	chr6:86178757-86179510	HCT-116	colon:	n/a	n/a
3	FOSL1	chr6:86178944-86179498	HCT-116	colon:	n/a	n/a
4	EP300	chr6:86178878-86179552	ECC-1	luminal epithelium:	n/a	chr6:86178956-86178964 chr6:86179006-86179020
5	NFIC	chr6:86178831-86179516	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr6:86178861-86179632	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
NT5E	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10944128	0.83[CHB][hapmap]
rs12212560	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2065114	0.86[CEU][hapmap]
rs2181187	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2229523	0.81[EUR][1000 genomes]
rs2758842	0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2758843	0.96[CHB][hapmap];1.00[JPT][hapmap]
rs2758845	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2842603	0.96[CHB][hapmap];1.00[JPT][hapmap]
rs2842614	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs4235826	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs4431401	0.83[CHB][hapmap]
rs4593336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4707207	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs6454467	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6454469	0.83[EUR][1000 genomes]
rs6454473	0.84[ASN][1000 genomes]
rs6909767	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6935918	0.96[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7742691	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7746065	0.91[CEU][hapmap]
rs7771612	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7775864	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs911927	0.96[CHB][hapmap];1.00[JPT][hapmap]
rs9342041	0.84[ASN][1000 genomes]
rs9344533	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9353320	0.89[ASN][1000 genomes]
rs9450282	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9450285	0.83[CHB][hapmap]
rs9450287	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9450302	0.96[CHB][hapmap];1.00[JPT][hapmap];0.83[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	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:18)

SNP	Gene	Cis/trans	Tissue	Source
rs4373337	SNHG5	cis	lung	GTEx
rs4373337	SNHG5	cis	Nerve Tibial	GTEx
rs4373337	C6orf160	cis	lesional skin	skin_eQTL
rs4373337	C6orf160	cis	normal skin	skin_eQTL
rs4373337	SNHG5	cis	Adipose Subcutaneous	GTEx
rs4373337	C6orf160	cis	uninvolved skin	skin_eQTL
rs4373337	SNHG5	cis	Whole Blood	GTEx
rs4373337	SNHG5	cis	Muscle Skeletal	GTEx
rs4373337	SNHG5	Cis_1M	lymphoblastoid	RTeQTL
rs4373337	NT5E	Cis_1M	lymphoblastoid	RTeQTL
rs4373337	SNHG5	cis	Esophagus Mucosa	GTEx
rs4373337	SNHG5	cis	Artery Tibial	GTEx
rs4373337	SNHG5	cis	multi-tissue	Pritchard
rs4373337	SNHG5	cis	Esophagus Muscularis	GTEx
rs4373337	SNHG5	cis	Skin Sun Exposed Lower leg	GTEx
rs4373337	SNHG5	cis	Thyroid	GTEx
rs4373337	SNHG5	cis	Artery Aorta	GTEx
rs4373337	SNHG5	cis	Heart Left Ventricle	GTEx

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86171800-86185200	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr6:86171800-86186000	Weak transcription	Fetal Stomach	stomach
3	chr6:86171800-86187600	Weak transcription	Colonic Mucosa	Colon
4	chr6:86172200-86179800	Weak transcription	Left Ventricle	heart
5	chr6:86172200-86186000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr6:86172400-86192800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr6:86174600-86180200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr6:86174800-86179800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr6:86174800-86180400	Weak transcription	Brain Anterior Caudate	brain
10	chr6:86175000-86180000	Genic enhancers	HSMM	muscle
11	chr6:86175200-86180000	Genic enhancers	Muscle Satellite Cultured Cells	--
12	chr6:86175400-86180000	Genic enhancers	NHEK	skin
13	chr6:86175400-86180200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr6:86175400-86180200	Genic enhancers	NHLF	lung
15	chr6:86175600-86191800	Weak transcription	Colon Smooth Muscle	Colon
16	chr6:86176000-86180600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr6:86176000-86183800	Genic enhancers	NHDF-Ad	bronchial
18	chr6:86176200-86183000	Weak transcription	Primary T cells from cord blood	blood
19	chr6:86176200-86187000	Strong transcription	Liver	Liver
20	chr6:86176200-86192400	Weak transcription	A549	lung
21	chr6:86176200-86192600	Weak transcription	HepG2	liver
22	chr6:86176600-86191400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr6:86176800-86242600	Weak transcription	Gastric	stomach
24	chr6:86177600-86182200	Enhancers	Placenta	Placenta
25	chr6:86177800-86179600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr6:86177800-86179800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr6:86177800-86180000	Genic enhancers	HMEC	breast
28	chr6:86177800-86180200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr6:86177800-86180400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr6:86177800-86180600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr6:86178000-86179600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr6:86178000-86179600	Enhancers	Hela-S3	cervix
33	chr6:86178000-86180000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr6:86178000-86180200	Enhancers	HSMMtube	muscle
35	chr6:86178000-86180400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr6:86178000-86180400	Genic enhancers	Fetal Muscle Leg	muscle
37	chr6:86178000-86183800	Genic enhancers	Osteobl	bone
38	chr6:86178400-86179600	Weak transcription	Stomach Smooth Muscle	stomach
39	chr6:86178400-86181600	Weak transcription	Aorta	Aorta
40	chr6:86178600-86179600	Strong transcription	HUVEC	blood vessel
41	chr6:86178600-86182800	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr6:86178800-86180200	Weak transcription	Fetal Muscle Trunk	muscle
43	chr6:86178800-86184000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr6:86178800-86206800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr6:86179000-86179600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr6:86179200-86180000	Enhancers	NH-A	brain
47	chr6:86179200-86180800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr6:86179200-86185600	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr6:86179400-86179600	Enhancers	Spleen	Spleen
50	chr6:86179400-86180000	Enhancers	Ovary	ovary

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