Variant report

Variant	rs2245430
Chromosome Location	chr17:18141705-18141706
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:18141114..18143286-chr17:18145998..18147564,2	K562	blood:
2	chr17:18136534..18138253-chr17:18140359..18142617,2	K562	blood:
3	chr17:18130743..18132299-chr17:18139265..18141956,2	K562	blood:
4	chr17:18139407..18141730-chr17:18142656..18144788,2	K562	blood:
5	chr17:18136077..18142771-chr17:18143654..18157956,22	MCF-7	breast:

Variant related genes	Relation type
ENSG00000131899	Chromatin interaction
ENSG00000177731	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12051649	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12946752	0.93[GIH][hapmap]
rs1563632	0.93[GIH][hapmap]
rs1563634	0.93[GIH][hapmap]
rs2071241	1.00[CEU][hapmap];0.87[GIH][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2075657	0.95[CHB][hapmap];0.84[EUR][1000 genomes]
rs2075658	0.80[EUR][1000 genomes]
rs2473656	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2605133	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2605141	0.93[GIH][hapmap]
rs2605144	0.93[GIH][hapmap]
rs2746029	0.81[TSI][hapmap]
rs2856289	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4925144	0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs59588957	0.81[EUR][1000 genomes]
rs712271	0.81[CHD][hapmap];0.83[GIH][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs712274	0.91[CHB][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes]
rs7225932	0.93[GIH][hapmap]
rs72831919	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs854773	0.83[GIH][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs854774	0.83[GIH][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs854777	0.90[CHD][hapmap];0.84[TSI][hapmap]
rs854778	0.81[EUR][1000 genomes]
rs854780	0.80[EUR][1000 genomes]
rs854783	0.80[EUR][1000 genomes]
rs854800	0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.80[EUR][1000 genomes]
rs854802	0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.80[EUR][1000 genomes]
rs854803	0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs9899249	0.91[CHB][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9903403	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9903591	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9913262	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[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	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	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
8	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
9	nsv907775	chr17:18108496-18206234	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
10	nsv543246	chr17:18121007-18165604	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
11	nsv9503	chr17:18121474-18169166	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
12	nsv907776	chr17:18122485-18170948	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
13	nsv1066718	chr17:18125122-18180807	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
14	nsv907777	chr17:18131087-18163262	Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2245430	TOP3A	cis	cerebellum	SCAN
rs2245430	SHMT1	cis	Esophagus Muscularis	GTEx
rs2245430	LOC162632	cis	parietal	SCAN
rs2245430	LOC162632	cis	cerebellum	SCAN
rs2245430	SHMT1	cis	lymphoblastoid	seeQTL
rs2245430	SHMT1	cis	Muscle Skeletal	GTEx
rs2245430	SHMT1	cis	Artery Tibial	GTEx
rs2245430	MYO15A	cis	cerebellum	SCAN
rs2245430	SHMT1	cis	Lymphoblastoid	GTEx
rs2245430	SHMT1	Cis_1M	lymphoblastoid	RTeQTL
rs2245430	SHMT1	cis	multi-tissue	Pritchard
rs2245430	SHMT1	cis	parietal	SCAN
rs2245430	SHMT1	cis	Whole Blood	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18129600-18148400	Weak transcription	Small Intestine	intestine
2	chr17:18130000-18145400	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr17:18130000-18148200	Weak transcription	Fetal Kidney	kidney
4	chr17:18130000-18148200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr17:18130000-18149200	Weak transcription	Psoas Muscle	Psoas
6	chr17:18130200-18145600	Weak transcription	A549	lung
7	chr17:18130200-18147000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr17:18130200-18147000	Weak transcription	Liver	Liver
9	chr17:18130200-18150800	Weak transcription	Right Atrium	heart
10	chr17:18130400-18142400	Weak transcription	Fetal Heart	heart
11	chr17:18130400-18146200	Weak transcription	NHDF-Ad	bronchial
12	chr17:18130400-18148200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr17:18130600-18148200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr17:18131200-18148400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr17:18134600-18149600	Strong transcription	Fetal Intestine Small	intestine
16	chr17:18134600-18150800	Weak transcription	Fetal Brain Male	brain
17	chr17:18134600-18150800	Strong transcription	Fetal Stomach	stomach
18	chr17:18134800-18142000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr17:18135000-18149400	Strong transcription	Fetal Muscle Trunk	muscle
20	chr17:18135200-18149400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr17:18135200-18149400	Strong transcription	Fetal Intestine Large	intestine
22	chr17:18135200-18149600	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr17:18135200-18150000	Strong transcription	Fetal Muscle Leg	muscle
24	chr17:18135200-18150600	Strong transcription	Brain Germinal Matrix	brain
25	chr17:18135200-18160000	Strong transcription	Fetal Brain Female	brain
26	chr17:18135400-18142600	Strong transcription	Dnd41	blood
27	chr17:18135400-18149800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
28	chr17:18135400-18150000	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr17:18135400-18150000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr17:18135400-18159600	Strong transcription	Primary T cells from cord blood	blood
31	chr17:18135400-18160200	Strong transcription	Thymus	Thymus
32	chr17:18135600-18141800	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr17:18135600-18142000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr17:18135600-18142600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr17:18135600-18149600	Strong transcription	Placenta	Placenta
36	chr17:18135600-18149800	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr17:18135600-18149800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr17:18135600-18150600	Strong transcription	Adipose Nuclei	Adipose
39	chr17:18135600-18159000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr17:18135600-18159400	Strong transcription	Fetal Lung	lung
41	chr17:18135600-18160000	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr17:18135800-18142000	Strong transcription	Right Ventricle	heart
43	chr17:18135800-18149600	Strong transcription	Gastric	stomach
44	chr17:18135800-18150000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr17:18135800-18150600	Strong transcription	Stomach Smooth Muscle	stomach
46	chr17:18135800-18160400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr17:18136000-18142000	Strong transcription	NHLF	lung
48	chr17:18136000-18142200	Strong transcription	H9 Cell Line	embryonic stem cell
49	chr17:18136000-18142600	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr17:18136000-18150000	Strong transcription	Ovary	ovary

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