Variant report

Variant	rs4924840
Chromosome Location	chr17:18104223-18104224
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:18087388..18090875-chr17:18103511..18106213,4	K562	blood:

Variant related genes	Relation type
ENSG00000266677	Chromatin interaction
ENSG00000091542	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11869205	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11870766	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11871970	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12150618	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12451754	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12936694	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12939469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12946842	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1378601	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1378602	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2360234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2605132	0.90[EUR][1000 genomes]
rs2605136	0.86[CHB][hapmap]
rs2605137	0.89[CEU][hapmap];0.88[CHB][hapmap];0.88[AMR][1000 genomes]
rs2746025	0.86[CHB][hapmap]
rs2746027	0.82[CEU][hapmap];0.86[CHB][hapmap];0.90[AMR][1000 genomes]
rs2746030	0.87[AMR][1000 genomes]
rs28641923	0.98[ASN][1000 genomes]
rs2925137	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2925138	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3794782	0.88[JPT][hapmap]
rs4603612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4924839	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4924841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925149	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4925150	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56021431	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs712270	0.93[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs712272	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs712273	0.87[ASN][1000 genomes]
rs712275	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7212808	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8071834	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs854771	0.81[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs854772	0.86[JPT][hapmap]
rs854775	0.88[JPT][hapmap]
rs854779	0.86[JPT][hapmap]
rs854781	0.88[JPT][hapmap]
rs854795	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs854797	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs854798	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs854799	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs854801	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs854804	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs854805	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs854806	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs854807	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs860567	0.92[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs860568	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs861278	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs865923	0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers 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 miRNA target site	116 gene(s)	inside rSNPs	diseases
4	nsv482491	chr17:17959577-18153920	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1061162	chr17:17978838-18259234	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv492305	chr17:17980441-18424702	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
7	nsv510702	chr17:18037676-18116801	Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv1062828	chr17:18098110-18136330	Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
9	nsv543245	chr17:18098110-18136330	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
10	nsv907773	chr17:18099962-18206234	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
11	nsv907774	chr17:18103907-18206234	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4924840	LLGL1	cis	Esophagus Mucosa	GTEx
rs4924840	RP11-258F1.1	cis	Esophagus Muscularis	GTEx
rs4924840	SHMT1	cis	Esophagus Muscularis	GTEx
rs4924840	ALKBH5	cis	Artery Tibial	GTEx
rs4924840	ALKBH5	cis	Esophagus Muscularis	GTEx
rs4924840	SHMT1	Cis_1M	lymphoblastoid	RTeQTL
rs4924840	SHMT1	cis	Artery Tibial	GTEx
rs4924840	LGALS9C	cis	Whole Blood	GTEx
rs4924840	SHMT1	cis	Muscle Skeletal	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18091200-18104600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr17:18091400-18114000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr17:18091800-18114400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr17:18094200-18114600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr17:18094400-18114600	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr17:18094600-18114600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr17:18095000-18108600	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr17:18095000-18114600	Strong transcription	Sigmoid Colon	Sigmoid Colon
9	chr17:18095000-18114800	Strong transcription	Fetal Thymus	thymus
10	chr17:18095400-18116000	Strong transcription	Fetal Stomach	stomach
11	chr17:18095600-18114600	Strong transcription	Dnd41	blood
12	chr17:18095800-18108600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr17:18096200-18114400	Strong transcription	Primary T cells from cord blood	blood
14	chr17:18096200-18114600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr17:18096400-18104800	Strong transcription	Hela-S3	cervix
16	chr17:18096800-18104400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr17:18096800-18114600	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr17:18097000-18105000	Strong transcription	A549	lung
19	chr17:18097000-18108600	Strong transcription	Brain Germinal Matrix	brain
20	chr17:18097000-18114600	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr17:18097200-18114600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr17:18097600-18114600	Strong transcription	Primary B cells from peripheral blood	blood
23	chr17:18097800-18104400	Strong transcription	Muscle Satellite Cultured Cells	--
24	chr17:18097800-18104800	Strong transcription	Primary hematopoietic stem cells	blood
25	chr17:18097800-18114600	Strong transcription	Fetal Brain Female	brain
26	chr17:18098000-18104600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr17:18098000-18105000	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr17:18098000-18114600	Strong transcription	Primary B cells from cord blood	blood
29	chr17:18098000-18114600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr17:18098000-18114600	Strong transcription	Fetal Muscle Leg	muscle
31	chr17:18098200-18105800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr17:18098200-18107400	Strong transcription	Fetal Lung	lung
33	chr17:18100600-18104600	Genic enhancers	Primary T cells fromperipheralblood	blood
34	chr17:18100800-18104800	Genic enhancers	Brain Inferior Temporal Lobe	brain
35	chr17:18100800-18104800	Genic enhancers	Right Ventricle	heart
36	chr17:18101000-18104600	Genic enhancers	Brain Cingulate Gyrus	brain
37	chr17:18101000-18108600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr17:18101200-18104400	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr17:18101200-18104400	Strong transcription	GM12878-XiMat	blood
40	chr17:18101200-18108400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr17:18101200-18114400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr17:18101600-18114600	Strong transcription	Thymus	Thymus
43	chr17:18101600-18115400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr17:18101800-18105600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr17:18101800-18105800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr17:18101800-18108200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr17:18101800-18108400	Weak transcription	Fetal Brain Male	brain
48	chr17:18101800-18109400	Weak transcription	HSMMtube	muscle
49	chr17:18102000-18108200	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr17:18102000-18108600	Weak transcription	K562	blood

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