Variant report

Variant	rs12946752
Chromosome Location	chr17:18176423-18176424
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr17:18164305..18167744-chr17:18176383..18179397,3	K562	blood:
2	chr17:18170342..18172549-chr17:18173949..18176436,3	MCF-7	breast:
3	chr17:18168768..18172845-chr17:18173287..18176443,4	K562	blood:
4	chr17:18174083..18176777-chr17:18181802..18184397,2	MCF-7	breast:
5	chr17:18171240..18173650-chr17:18173908..18177269,4	MCF-7	breast:
6	chr17:18173874..18176766-chr17:18191983..18193813,2	K562	blood:
7	chr17:18174943..18176690-chr17:18181695..18183863,2	K562	blood:
8	chr17:18173960..18176627-chr17:18178120..18180882,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SMCR7-2	chr17:18176224-18176969	NONHSAT146170

No data

Variant related genes	Relation type
ENSG00000177302	Chromatin interaction
ENSG00000260647	Chromatin interaction
ENSG00000177427	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12950117	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1563632	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]
rs1563634	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1682280	0.80[LWK][hapmap];0.83[TSI][hapmap]
rs2071241	0.82[ASW][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs2245430	0.93[GIH][hapmap]
rs2273027	0.87[JPT][hapmap]
rs2473656	0.93[GIH][hapmap]
rs2605141	1.00[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];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2605143	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2605144	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2605145	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764404	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4924846	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4925144	0.87[GIH][hapmap]
rs4925166	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4925179	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs641028	0.81[AMR][1000 genomes]
rs6502647	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs6502650	0.83[AMR][1000 genomes]
rs669340	1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap]
rs712274	0.86[GIH][hapmap]
rs7212104	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7225932	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8065874	0.82[JPT][hapmap]
rs8076253	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs854800	0.84[GIH][hapmap]
rs854802	0.84[GIH][hapmap]
rs854803	0.84[GIH][hapmap]
rs921985	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs12946752	LOC162632	cis	parietal	SCAN
rs12946752	SHMT1	cis	Lymphoblastoid	GTEx
rs12946752	SHMT1	cis	parietal	SCAN
rs12946752	USP32P2	cis	Whole Blood	GTEx
rs12946752	SHMT1	Cis_1M	lymphoblastoid	RTeQTL
rs12946752	SHMT1	cis	lymphoblastoid	seeQTL
rs12946752	SHMT1	cis	Whole Blood	GTEx
rs12946752	FAM106A	cis	Thyroid	GTEx
rs12946752	LGALS9C	cis	Whole Blood	GTEx
rs12946752	SHMT1	cis	multi-tissue	Pritchard
rs12946752	SHMT1	cis	Esophagus Muscularis	GTEx
rs12946752	SHMT1	cis	Muscle Skeletal	GTEx
rs12946752	SHMT1	cis	Artery Tibial	GTEx
rs12946752	TOP3A	cis	cerebellum	SCAN
rs12946752	LOC162632	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18165000-18176600	Weak transcription	HUVEC	blood vessel
2	chr17:18165400-18177600	Weak transcription	Small Intestine	intestine
3	chr17:18165600-18181400	Weak transcription	Psoas Muscle	Psoas
4	chr17:18165800-18182800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr17:18166000-18179600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr17:18166000-18183800	Weak transcription	Fetal Brain Male	brain
7	chr17:18166200-18183600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr17:18166400-18182600	Strong transcription	Fetal Brain Female	brain
9	chr17:18167000-18188200	Weak transcription	Stomach Mucosa	stomach
10	chr17:18168800-18177600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr17:18168800-18179200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr17:18168800-18179400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr17:18168800-18183200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr17:18169000-18176600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr17:18169000-18176600	Weak transcription	HepG2	liver
16	chr17:18169000-18176600	Weak transcription	HSMMtube	muscle
17	chr17:18169000-18177600	Weak transcription	Aorta	Aorta
18	chr17:18169000-18177600	Weak transcription	Esophagus	oesophagus
19	chr17:18169000-18177600	Weak transcription	Gastric	stomach
20	chr17:18169000-18177600	Weak transcription	Ovary	ovary
21	chr17:18169000-18177600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr17:18169000-18177600	Weak transcription	Right Ventricle	heart
23	chr17:18169000-18181200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr17:18169200-18176600	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr17:18169200-18177400	Weak transcription	Primary B cells from peripheral blood	blood
26	chr17:18169200-18177400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr17:18169200-18177600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr17:18169200-18177600	Weak transcription	Left Ventricle	heart
29	chr17:18169200-18177600	Weak transcription	Pancreas	Pancrea
30	chr17:18169200-18179400	Weak transcription	NHDF-Ad	bronchial
31	chr17:18169400-18177600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr17:18169600-18177400	Weak transcription	Colon Smooth Muscle	Colon
33	chr17:18171000-18183800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr17:18172000-18177600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr17:18172200-18176600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr17:18172200-18176600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr17:18172200-18176600	Weak transcription	Fetal Lung	lung
38	chr17:18172200-18177200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr17:18172200-18217400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr17:18172400-18176600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr17:18172400-18201000	Strong transcription	Fetal Stomach	stomach
42	chr17:18172600-18181800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr17:18172800-18198400	Strong transcription	Thymus	Thymus
44	chr17:18173000-18198400	Strong transcription	Fetal Thymus	thymus
45	chr17:18173000-18199000	Strong transcription	Primary T cells from cord blood	blood
46	chr17:18173000-18200400	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr17:18173000-18213800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr17:18173200-18198400	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr17:18173200-18200200	Strong transcription	Placenta	Placenta
50	chr17:18173400-18183600	Weak transcription	Fetal Heart	heart

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