Variant report

Variant	rs12431818
Chromosome Location	chr14:35239689-35239690
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:35237218..35239739-chr14:35251859..35254380,2	K562	blood:
2	chr14:35237464..35239910-chr14:35248990..35251298,2	K562	blood:
3	chr14:35239285..35241333-chr14:35342948..35344948,2	MCF-7	breast:
4	chr14:35239089..35240652-chr14:35244321..35246894,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258738	Chromatin interaction
ENSG00000198604	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10136352	0.81[JPT][hapmap]
rs10150083	0.80[CHB][hapmap];0.83[JPT][hapmap];0.85[EUR][1000 genomes]
rs10150856	0.81[ASN][1000 genomes]
rs11847610	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1200414	0.81[JPT][hapmap]
rs12432567	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12433706	0.87[CHB][hapmap];0.90[JPT][hapmap];0.91[LWK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs12435778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12435859	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12586459	0.84[ASN][1000 genomes]
rs12586462	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12587021	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs12587251	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12587390	0.87[CHB][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12587913	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12588318	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12590112	0.90[JPT][hapmap]
rs12590268	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13379337	0.82[CHB][hapmap]
rs1400745	0.90[JPT][hapmap]
rs17102726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17102768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17102795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17102829	0.83[CEU][hapmap];0.90[JPT][hapmap]
rs17526787	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs17526884	0.91[YRI][hapmap];0.93[AFR][1000 genomes]
rs1959154	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2295468	0.82[ASN][1000 genomes]
rs2383675	0.80[LWK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2383676	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2383677	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap]
rs34072166	0.87[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34245772	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3783315	0.89[ASW][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs3783316	0.81[JPT][hapmap]
rs5016735	1.00[ASN][1000 genomes]
rs55979964	0.90[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs58268256	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58587072	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59092668	0.87[AFR][1000 genomes]
rs59678582	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61981198	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61981200	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61981202	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61981204	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61981228	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61981232	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61981234	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61981236	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61981237	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61988010	0.91[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs61988011	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61988012	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61988013	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61988044	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61988045	0.84[ASN][1000 genomes]
rs7142012	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7148400	0.81[JPT][hapmap]
rs7150069	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7153289	0.95[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7155348	0.98[ASN][1000 genomes]
rs8005470	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs8005659	0.89[ASW][hapmap];0.95[CEU][hapmap];0.87[CHB][hapmap];0.92[LWK][hapmap];0.93[MEX][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs8009900	0.84[AFR][1000 genomes]
rs8010504	0.97[ASN][1000 genomes]
rs8010579	0.87[CHB][hapmap]
rs8016548	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12431818	SCFD1	cis	cerebellum	SCAN
rs12431818	SNX6	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	chr14:35221600-35255400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr14:35221600-35258800	Strong transcription	Dnd41	blood
10	chr14:35221600-35274600	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr14:35224000-35240400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr14:35226000-35273400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr14:35226000-35274000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr14:35226200-35252600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr14:35226400-35267000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr14:35227600-35255600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr14:35227600-35267000	Weak transcription	Stomach Mucosa	stomach
18	chr14:35228000-35264600	Weak transcription	Brain Substantia Nigra	brain
19	chr14:35230000-35267000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr14:35230600-35241800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr14:35230600-35242000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr14:35230600-35250000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr14:35231200-35291800	Weak transcription	Fetal Brain Male	brain
24	chr14:35232000-35241800	Weak transcription	Esophagus	oesophagus
25	chr14:35232000-35269800	Weak transcription	Fetal Heart	heart
26	chr14:35232600-35267200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr14:35232600-35293200	Weak transcription	Fetal Kidney	kidney
28	chr14:35233000-35251400	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr14:35233800-35241800	Weak transcription	Fetal Intestine Small	intestine
30	chr14:35234000-35248000	Weak transcription	Colonic Mucosa	Colon
31	chr14:35234000-35252800	Weak transcription	Colon Smooth Muscle	Colon
32	chr14:35234200-35240200	Weak transcription	Placenta	Placenta
33	chr14:35234200-35240200	Weak transcription	Fetal Stomach	stomach
34	chr14:35234200-35241400	Weak transcription	Ovary	ovary
35	chr14:35234200-35244600	Weak transcription	Right Ventricle	heart
36	chr14:35234200-35244600	Weak transcription	NHLF	lung
37	chr14:35234200-35267000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr14:35234200-35267000	Weak transcription	Pancreas	Pancrea
39	chr14:35234200-35271400	Weak transcription	Brain Angular Gyrus	brain
40	chr14:35234200-35271400	Weak transcription	Brain Anterior Caudate	brain
41	chr14:35234200-35274200	Weak transcription	Aorta	Aorta
42	chr14:35234200-35276000	Weak transcription	Brain Hippocampus Middle	brain
43	chr14:35234200-35311600	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr14:35234400-35239800	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr14:35234400-35239800	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr14:35234400-35239800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr14:35234400-35240000	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr14:35234400-35240200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr14:35234400-35240200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr14:35234400-35240200	Weak transcription	Fetal Intestine Large	intestine

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