Variant report

Variant	rs4925169
Chromosome Location	chr17:18222341-18222342
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:18222213-18222341	HepG2	liver:	n/a	n/a
2	POLR2A	chr17:18222131-18222606	HepG2	liver:	n/a	n/a
3	POLR2A	chr17:18222229-18222443	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr17:18222116-18222535	GM12892	blood:	n/a	n/a
5	POLR2A	chr17:18222037-18222917	GM12878	blood:	n/a	n/a
6	POLR2A	chr17:18221933-18222678	K562	blood:	n/a	n/a
7	POLR2A	chr17:18222107-18222495	GM12891	blood:	n/a	n/a
8	POLR2A	chr17:18222259-18222511	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:18142816..18144469-chr17:18222241..18223904,2	K562	blood:
2	chr17:18222298..18225183-chr17:18254419..18256749,2	MCF-7	breast:
3	chr17:18217609..18225680-chr17:18226125..18232187,14	K562	blood:
4	chr17:18159194..18166260-chr17:18215929..18222740,16	MCF-7	breast:
5	chr17:18160479..18164858-chr17:18221003..18224877,4	MCF-7	breast:
6	chr17:18151039..18153788-chr17:18220969..18222731,2	MCF-7	breast:

No data

Variant related genes	Relation type
TOP3A	TF binding region
ENSG00000267350	Chromatin interaction
ENSG00000177427	Chromatin interaction
ENSG00000177731	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs11868259	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11870126	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12936652	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12936769	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12937300	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12939092	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12939259	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12939357	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12939757	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12945597	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12946058	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12949078	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12949983	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12952556	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12952667	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1563631	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1563633	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1979276	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1979277	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2230154	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2273028	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2273030	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2386456	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2386457	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2386458	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2605142	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2746023	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2746024	0.91[ASN][1000 genomes]
rs28419113	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3764405	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3783	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3794771	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3794772	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3829583	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4632181	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4924750	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4924842	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4924843	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4924845	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924847	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4924849	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4925160	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4925162	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4925163	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4925167	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4925171	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4925172	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58215032	0.87[EUR][1000 genomes]
rs6502643	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6502644	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6502646	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6502649	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66903818	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7207123	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7207306	0.85[ASN][1000 genomes]
rs7215839	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7222684	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7223122	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8068602	0.85[EUR][1000 genomes]
rs8068854	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8070633	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8071231	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8073464	0.82[EUR][1000 genomes]
rs8074444	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8080966	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs921865	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs921866	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs921986	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs941451	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9898631	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv833386	chr17:18170261-18332726	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv1057081	chr17:18171516-18256347	Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv543247	chr17:18171516-18256347	Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv1062368	chr17:18180747-18259234	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv833387	chr17:18200081-18378155	Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS 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	34 gene(s)	inside rSNPs	diseases
10	esv1806346	chr17:18200081-18446384	Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
11	esv1812661	chr17:18200081-18446384	Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
12	nsv428333	chr17:18200081-18446384	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' 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	39 gene(s)	inside rSNPs	diseases
13	nsv427992	chr17:18200081-19192047	Strong transcription Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
14	nsv521075	chr17:18220770-18227081	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4925169	SHMT1	cis	multi-tissue	Pritchard
rs4925169	RP11-258F1.1	cis	Adipose Subcutaneous	GTEx
rs4925169	SHMT1	Cis_1M	lymphoblastoid	RTeQTL
rs4925169	SHMT1	cis	Esophagus Muscularis	GTEx
rs4925169	LGALS9C	cis	Whole Blood	GTEx
rs4925169	SHMT1	cis	Muscle Skeletal	GTEx
rs4925169	SHMT1	cis	Artery Tibial	GTEx
rs4925169	LLGL1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18219400-18224200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr17:18219400-18224200	Enhancers	Fetal Brain Male	brain
3	chr17:18219400-18224400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr17:18219400-18224800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr17:18219400-18227200	Genic enhancers	Primary T cells fromperipheralblood	blood
6	chr17:18219400-18266000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr17:18219600-18222400	Genic enhancers	Fetal Thymus	thymus
8	chr17:18219600-18222400	Genic enhancers	HMEC	breast
9	chr17:18219600-18223600	Genic enhancers	Fetal Lung	lung
10	chr17:18219600-18223600	Genic enhancers	Fetal Muscle Leg	muscle
11	chr17:18219600-18223600	Genic enhancers	Fetal Stomach	stomach
12	chr17:18219600-18223800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr17:18219600-18224200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr17:18219600-18224200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr17:18219600-18224200	Genic enhancers	Liver	Liver
16	chr17:18219600-18224200	Genic enhancers	Fetal Muscle Trunk	muscle
17	chr17:18219600-18224200	Genic enhancers	Left Ventricle	heart
18	chr17:18219600-18224400	Genic enhancers	Placenta	Placenta
19	chr17:18219600-18224600	Enhancers	Right Atrium	heart
20	chr17:18219600-18224800	Genic enhancers	Primary B cells from peripheral blood	blood
21	chr17:18219600-18225000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr17:18219600-18226000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr17:18219800-18222400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr17:18219800-18223600	Genic enhancers	Brain Hippocampus Middle	brain
25	chr17:18219800-18223800	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr17:18219800-18223800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr17:18219800-18223800	Genic enhancers	Lung	lung
28	chr17:18219800-18223800	Genic enhancers	NHEK	skin
29	chr17:18219800-18224200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr17:18219800-18224200	Genic enhancers	Esophagus	oesophagus
31	chr17:18219800-18224200	Enhancers	Fetal Heart	heart
32	chr17:18219800-18224400	Genic enhancers	Spleen	Spleen
33	chr17:18219800-18224800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
34	chr17:18219800-18225000	Genic enhancers	Cortex derived primary cultured neurospheres	brain
35	chr17:18219800-18226000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr17:18220000-18222800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr17:18220000-18223000	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr17:18220000-18223600	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr17:18220000-18224200	Genic enhancers	Colonic Mucosa	Colon
40	chr17:18220000-18224200	Genic enhancers	Rectal Mucosa Donor 31	rectum
41	chr17:18220000-18224800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr17:18220000-18226000	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr17:18220200-18222600	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr17:18220200-18228000	Weak transcription	Fetal Kidney	kidney
45	chr17:18220400-18224200	Genic enhancers	Ovary	ovary
46	chr17:18220400-18228000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr17:18220600-18222400	Genic enhancers	HUVEC	blood vessel
48	chr17:18220600-18223800	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
49	chr17:18220600-18224200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr17:18220600-18224800	Genic enhancers	Right Ventricle	heart

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