Variant report

Variant	rs12433706
Chromosome Location	chr14:35234894-35234895
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF7L2	chr14:35234724-35234966	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:35019137..35020709-chr14:35232783..35235542,2	MCF-7	breast:
2	chr14:35022083..35024389-chr14:35233897..35236737,2	MCF-7	breast:
3	chr14:35232989..35235688-chr14:35236337..35238801,2	K562	blood:

Variant related genes	Relation type
BAZ1A	TF binding region

Extended variants
information (count: 65 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10136352	0.90[JPT][hapmap]
rs10145299	0.92[ASN][1000 genomes]
rs10147130	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10147134	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10150083	0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[ASN][1000 genomes]
rs10150856	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11847610	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1200414	0.90[JPT][hapmap]
rs12431818	0.87[CHB][hapmap];0.90[JPT][hapmap];0.91[LWK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs12435778	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs12435859	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12587021	0.96[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12587251	0.95[AFR][1000 genomes]
rs12587390	0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12590112	0.84[CEU][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs13379337	0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs17102726	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs17102768	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs17102795	0.85[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs17102829	1.00[JPT][hapmap]
rs17526787	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17526884	0.91[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1959154	0.93[AFR][1000 genomes]
rs2383675	0.88[LWK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2383677	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34072166	0.81[CHB][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.90[MKK][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes]
rs3783315	0.89[ASW][hapmap];0.96[CEU][hapmap];0.81[CHB][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes]
rs3783316	0.90[JPT][hapmap]
rs5016735	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55979964	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs56975955	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58074336	0.97[ASN][1000 genomes]
rs58268256	0.90[AFR][1000 genomes]
rs58587072	0.83[AFR][1000 genomes]
rs59092668	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59678582	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61981201	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61981204	0.81[ASN][1000 genomes]
rs61981228	0.89[AFR][1000 genomes]
rs61988010	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs61988011	0.95[AFR][1000 genomes]
rs61988013	0.90[AFR][1000 genomes]
rs6571686	0.97[ASN][1000 genomes]
rs7148400	0.90[JPT][hapmap]
rs7150069	0.81[CHB][hapmap];0.89[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7153289	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7155348	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8005470	0.96[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes]
rs8005659	0.89[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs8007644	0.97[ASN][1000 genomes]
rs8009900	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8010504	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8010579	1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs8013484	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8016548	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs8017454	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8019856	0.88[CHB][hapmap];0.81[JPT][hapmap]

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	nsv1040980	chr14:34345018-35255592	Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv1048408	chr14:34958352-35255592	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	esv3392700	chr14:34989406-35365530	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	nsv1041857	chr14:35084889-35417180	Strong transcription Enhancers Weak transcription Flanking Active TSS 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 miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv1040350	chr14:35196524-35245409	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv1051540	chr14:35200858-35278635	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv517328	chr14:35229680-35234894	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv523492	chr14:35229680-35242828	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12433706	SCFD1	cis	cerebellum	SCAN
rs12433706	SNX6	cis	parietal	SCAN
rs12433706	NUBPL	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:35219400-35262000	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr14:35219400-35267000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr14:35219600-35254600	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr14:35221000-35253200	Strong transcription	Primary B cells from peripheral blood	blood
5	chr14:35221000-35255800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr14:35221200-35262000	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr14:35221400-35280800	Strong transcription	Primary T helper cells PMA-I stimulated	--
8	chr14:35221600-35235400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr14:35221600-35237400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr14:35221600-35237800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr14:35221600-35255400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr14:35221600-35258800	Strong transcription	Dnd41	blood
13	chr14:35221600-35274600	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr14:35222600-35236200	Strong transcription	Primary T cells from cord blood	blood
15	chr14:35222600-35237200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr14:35224000-35240400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr14:35225600-35237200	Strong transcription	Fetal Thymus	thymus
18	chr14:35226000-35273400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr14:35226000-35274000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr14:35226200-35252600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr14:35226400-35267000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr14:35227000-35235400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr14:35227200-35237200	Strong transcription	A549	lung
24	chr14:35227400-35235800	Strong transcription	Fetal Brain Female	brain
25	chr14:35227400-35236000	Strong transcription	GM12878-XiMat	blood
26	chr14:35227600-35255600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr14:35227600-35267000	Weak transcription	Stomach Mucosa	stomach
28	chr14:35227800-35237200	Strong transcription	Primary B cells from cord blood	blood
29	chr14:35228000-35264600	Weak transcription	Brain Substantia Nigra	brain
30	chr14:35228200-35236000	Strong transcription	HepG2	liver
31	chr14:35229000-35235600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
32	chr14:35229000-35235800	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr14:35229200-35235600	Strong transcription	Primary hematopoietic stem cells	blood
34	chr14:35229200-35235600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr14:35230000-35267000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr14:35230400-35235600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr14:35230600-35236000	Strong transcription	K562	blood
38	chr14:35230600-35241800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr14:35230600-35242000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr14:35230600-35250000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr14:35231200-35291800	Weak transcription	Fetal Brain Male	brain
42	chr14:35231800-35235400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr14:35232000-35241800	Weak transcription	Esophagus	oesophagus
44	chr14:35232000-35269800	Weak transcription	Fetal Heart	heart
45	chr14:35232600-35235000	Strong transcription	Hela-S3	cervix
46	chr14:35232600-35235600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr14:35232600-35267200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr14:35232600-35293200	Weak transcription	Fetal Kidney	kidney
49	chr14:35233000-35251400	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr14:35233200-35235600	Weak transcription	Psoas Muscle	Psoas

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