Variant report

Variant	rs12697457
Chromosome Location	chr5:43551810-43551811
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:43531285..43533909-chr5:43551302..43554401,3	K562	blood:
2	chr5:43551318..43553577-chr5:43601247..43603136,2	K562	blood:
3	chr5:43547644..43550345-chr5:43550491..43552259,2	MCF-7	breast:
4	chr5:43483169..43485499-chr5:43549794..43552040,2	MCF-7	breast:
5	chr5:43482574..43484301-chr5:43550900..43553223,2	K562	blood:
6	chr5:43482801..43486073-chr5:43545843..43553223,8	K562	blood:

Variant related genes	Relation type
ENSG00000151881	Chromatin interaction
ENSG00000172239	Chromatin interaction
ENSG00000112992	Chromatin interaction
ENSG00000249492	Chromatin interaction
ENSG00000248092	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10036954	0.88[ASN][1000 genomes]
rs10038545	0.81[EUR][1000 genomes]
rs10053229	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10054519	0.82[EUR][1000 genomes]
rs10059912	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10059993	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10065689	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10066408	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10068064	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10462051	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10472380	0.81[EUR][1000 genomes]
rs11949083	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11952832	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11958046	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12332560	1.00[ASN][1000 genomes]
rs12521249	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12651879	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs13189484	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13359906	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13360902	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1366410	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1389870	0.82[EUR][1000 genomes]
rs2131998	0.82[EUR][1000 genomes]
rs2132003	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28437972	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28606458	0.86[ASN][1000 genomes]
rs3776423	0.88[ASN][1000 genomes]
rs4072918	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4072919	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4074777	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4331909	0.96[ASN][1000 genomes]
rs4386738	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4428418	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4467713	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4535459	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4610465	0.90[EUR][1000 genomes]
rs4866833	0.96[ASN][1000 genomes]
rs4866835	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55667604	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55855322	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56008952	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56097465	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56252541	0.82[ASN][1000 genomes]
rs56333629	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57403343	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59001943	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs59224335	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60297702	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6451697	0.82[EUR][1000 genomes]
rs6451699	0.82[EUR][1000 genomes]
rs6451704	0.81[ASN][1000 genomes]
rs6451705	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6451712	0.96[ASN][1000 genomes]
rs66495712	0.82[EUR][1000 genomes]
rs67261887	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67466542	0.88[ASN][1000 genomes]
rs67581152	0.98[ASN][1000 genomes]
rs6860493	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6866325	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6866802	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6869933	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6878770	0.82[EUR][1000 genomes]
rs6884661	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6885679	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6891363	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6895327	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6896693	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6898866	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72756535	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7705166	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7706431	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7710628	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7713479	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7715782	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7717636	1.00[ASN][1000 genomes]
rs7718627	0.82[EUR][1000 genomes]
rs7732656	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7736108	0.82[EUR][1000 genomes]
rs7736615	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7737793	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9687341	0.90[ASN][1000 genomes]
rs9885189	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881017	chr5:43444826-43731692	Weak transcription Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	222 gene(s)	inside rSNPs	diseases
2	nsv830275	chr5:43469511-43639384	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription 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 miRNA target site	220 gene(s)	inside rSNPs	diseases
3	esv1835057	chr5:43515280-43557405	Active TSS Flanking Active TSS Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
4	esv1835614	chr5:43515280-43561759	Genic enhancers Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
5	esv1837000	chr5:43515280-43561759	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
6	nsv881108	chr5:43527432-43800333	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
7	esv3471239	chr5:43541792-43587904	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
8	esv3471240	chr5:43541792-43587904	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12697457	NNT	cis	multi-tissue	Pritchard
rs12697457	NNT	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43523200-43552200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr5:43523400-43553600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
3	chr5:43523400-43554600	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr5:43523600-43554200	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr5:43524000-43555200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr5:43524200-43553600	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr5:43524800-43553600	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr5:43525000-43552400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr5:43525400-43553400	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr5:43526000-43553200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr5:43526000-43554200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:43527200-43552000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr5:43527200-43552400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr5:43527400-43552400	Strong transcription	Hela-S3	cervix
15	chr5:43527400-43554200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr5:43527600-43553200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr5:43527600-43554400	Strong transcription	Primary B cells from peripheral blood	blood
18	chr5:43527600-43555600	Strong transcription	Fetal Thymus	thymus
19	chr5:43527600-43556000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr5:43527800-43552400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr5:43528000-43554800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr5:43530200-43552000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr5:43532200-43552200	Strong transcription	Duodenum Mucosa	Duodenum
24	chr5:43532800-43552400	Strong transcription	Fetal Intestine Large	intestine
25	chr5:43532800-43554000	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr5:43534600-43554400	Weak transcription	Aorta	Aorta
27	chr5:43534800-43554000	Weak transcription	Right Ventricle	heart
28	chr5:43535000-43553600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr5:43538000-43553600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr5:43538800-43554600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr5:43539800-43554200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr5:43540000-43552200	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr5:43541000-43554200	Weak transcription	Stomach Mucosa	stomach
34	chr5:43542800-43552200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr5:43542800-43556000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr5:43542800-43556000	Weak transcription	Esophagus	oesophagus
37	chr5:43543800-43552600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr5:43544400-43554200	Strong transcription	Primary B cells from cord blood	blood
39	chr5:43544400-43554200	Strong transcription	NHLF	lung
40	chr5:43547000-43552600	Weak transcription	Rectal Smooth Muscle	rectum
41	chr5:43547200-43552200	Weak transcription	NHEK	skin
42	chr5:43547600-43555200	Weak transcription	Colonic Mucosa	Colon
43	chr5:43547800-43552200	Weak transcription	Brain Substantia Nigra	brain
44	chr5:43547800-43552200	Weak transcription	Fetal Brain Male	brain
45	chr5:43547800-43552200	Weak transcription	Psoas Muscle	Psoas
46	chr5:43547800-43553200	Weak transcription	Small Intestine	intestine
47	chr5:43547800-43553800	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr5:43547800-43554200	Weak transcription	Stomach Smooth Muscle	stomach
49	chr5:43547800-43554800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr5:43547800-43556000	Weak transcription	Gastric	stomach

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