Variant report

Variant	rs1563632
Chromosome Location	chr17:18220770-18220771
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:18220203-18221689	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:18138823..18141039-chr17:18218928..18220976,2	MCF-7	breast:
2	chr17:18209725..18212720-chr17:18219456..18221596,2	MCF-7	breast:
3	chr17:18086084..18087983-chr17:18217517..18220819,3	MCF-7	breast:
4	chr17:18118058..18120854-chr17:18219963..18222284,2	K562	blood:
5	chr17:18217609..18225680-chr17:18226125..18232187,14	K562	blood:
6	chr17:18159194..18166260-chr17:18215929..18222740,16	MCF-7	breast:
7	chr17:18218839..18221214-chr17:18276166..18278374,2	MCF-7	breast:

No data

Variant related genes	Relation type
TOP3A	TF binding region
ENSG00000177302	Chromatin interaction
ENSG00000266677	Chromatin interaction
ENSG00000267350	Chromatin interaction
ENSG00000177731	Chromatin interaction
ENSG00000091542	Chromatin interaction
ENSG00000177427	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs12946752	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12950117	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1563634	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1682280	0.80[LWK][hapmap];0.83[TSI][hapmap]
rs2071241	0.86[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs2245430	0.93[GIH][hapmap]
rs2273027	0.82[JPT][hapmap]
rs2473656	0.93[GIH][hapmap]
rs2605141	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2605143	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2605144	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2605145	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2688030	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2688036	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs28597812	0.83[ASN][1000 genomes]
rs3764404	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4924846	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4925144	0.87[GIH][hapmap]
rs4925166	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4925179	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs638416	0.80[ASN][1000 genomes]
rs641028	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6502647	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs6502650	0.82[AMR][1000 genomes]
rs669340	1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.84[ASN][1000 genomes]
rs712274	0.86[GIH][hapmap]
rs7212104	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7225932	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8076253	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs854800	0.84[GIH][hapmap]
rs854802	0.84[GIH][hapmap]
rs854803	0.84[GIH][hapmap]
rs921985	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[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:20)

SNP	Gene	Cis/trans	Tissue	Source
rs1563632	ENST00000300223	cis	multi-tissue	Pritchard
rs1563632	LGALS9C	cis	Whole Blood	GTEx
rs1563632	SHMT1	cis	Artery Tibial	GTEx
rs1563632	SHMT1	cis	Esophagus Muscularis	GTEx
rs1563632	NM_182568	cis	multi-tissue	Pritchard
rs1563632	SHMT1	cis	lymphoblastoid	seeQTL
rs1563632	USP32P2	cis	Whole Blood	GTEx
rs1563632	SHMT1	cis	multi-tissue	Pritchard
rs1563632	SHMT1	cis	parietal	SCAN
rs1563632	TOP3A	cis	cerebellum	SCAN
rs1563632	SHMT1	cis	Whole Blood	GTEx
rs1563632	SHMT1	cis	Muscle Skeletal	GTEx
rs1563632	ATPAF2	cis	multi-tissue	Pritchard
rs1563632	LOC162632	cis	cerebellum	SCAN
rs1563632	SHMT1	Cis_1M	lymphoblastoid	RTeQTL
rs1563632	SHMT1	cis	Liver	GTEx
rs1563632	C15orf50	trans	multi-tissue	Pritchard
rs1563632	LOC162632	cis	parietal	SCAN
rs1563632	FAM106A	cis	Thyroid	GTEx
rs1563632	FAM83G	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18218600-18221200	ZNF genes & repeats	Fetal Intestine Large	intestine
2	chr17:18218600-18221600	Transcr. at gene 5' and 3'	Dnd41	blood
3	chr17:18218800-18222200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr17:18219000-18221800	ZNF genes & repeats	Fetal Intestine Small	intestine
5	chr17:18219400-18220800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr17:18219400-18220800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr17:18219400-18221800	Enhancers	Small Intestine	intestine
8	chr17:18219400-18224200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr17:18219400-18224200	Enhancers	Fetal Brain Male	brain
10	chr17:18219400-18224400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr17:18219400-18224800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr17:18219400-18227200	Genic enhancers	Primary T cells fromperipheralblood	blood
13	chr17:18219400-18266000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr17:18219600-18220800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr17:18219600-18220800	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr17:18219600-18220800	Genic enhancers	Adipose Nuclei	Adipose
17	chr17:18219600-18220800	Weak transcription	Aorta	Aorta
18	chr17:18219600-18220800	Enhancers	Pancreas	Pancrea
19	chr17:18219600-18221000	Genic enhancers	Brain Inferior Temporal Lobe	brain
20	chr17:18219600-18221600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr17:18219600-18221800	Genic enhancers	Thymus	Thymus
22	chr17:18219600-18222200	Enhancers	Placenta Amnion	Placenta Amnion
23	chr17:18219600-18222400	Genic enhancers	Fetal Thymus	thymus
24	chr17:18219600-18222400	Genic enhancers	HMEC	breast
25	chr17:18219600-18223600	Genic enhancers	Fetal Lung	lung
26	chr17:18219600-18223600	Genic enhancers	Fetal Muscle Leg	muscle
27	chr17:18219600-18223600	Genic enhancers	Fetal Stomach	stomach
28	chr17:18219600-18223800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr17:18219600-18224200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr17:18219600-18224200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr17:18219600-18224200	Genic enhancers	Liver	Liver
32	chr17:18219600-18224200	Genic enhancers	Fetal Muscle Trunk	muscle
33	chr17:18219600-18224200	Genic enhancers	Left Ventricle	heart
34	chr17:18219600-18224400	Genic enhancers	Placenta	Placenta
35	chr17:18219600-18224600	Enhancers	Right Atrium	heart
36	chr17:18219600-18224800	Genic enhancers	Primary B cells from peripheral blood	blood
37	chr17:18219600-18225000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr17:18219600-18226000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr17:18219800-18220800	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr17:18219800-18220800	Genic enhancers	Primary B cells from cord blood	blood
41	chr17:18219800-18220800	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr17:18219800-18220800	Weak transcription	HSMMtube	muscle
43	chr17:18219800-18220800	Strong transcription	NH-A	brain
44	chr17:18219800-18221000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr17:18219800-18221000	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr17:18219800-18221000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr17:18219800-18221000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr17:18219800-18221000	Genic enhancers	Brain Germinal Matrix	brain
49	chr17:18219800-18221000	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr17:18219800-18221000	Enhancers	Pancreatic Islets	Pancreatic Islet

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