Variant report

Variant	rs12588458
Chromosome Location	chr14:67830856-67830857
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:67829435..67831419-chr14:67848497..67850545,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134001	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs1006595	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.83[ASN][1000 genomes]
rs10129185	0.93[ASN][1000 genomes]
rs10132093	0.94[CHB][hapmap];0.88[JPT][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10137557	0.80[CHB][hapmap]
rs10138824	0.81[GIH][hapmap]
rs10139953	0.90[ASN][1000 genomes]
rs10141180	0.86[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10141879	0.81[GIH][hapmap]
rs10144090	0.81[GIH][hapmap]
rs10144122	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10144401	0.81[GIH][hapmap]
rs10144417	0.80[CHD][hapmap];0.83[GIH][hapmap]
rs10144774	0.93[ASN][1000 genomes]
rs10146389	0.83[ASN][1000 genomes]
rs10146663	0.81[GIH][hapmap]
rs10147362	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10149615	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10150902	0.81[GIH][hapmap]
rs10431718	0.81[GIH][hapmap]
rs1044745	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1045060	0.80[CHD][hapmap];0.81[GIH][hapmap]
rs1073605	0.95[EUR][1000 genomes]
rs1078194	1.00[CEU][hapmap]
rs11158653	0.81[GIH][hapmap];0.87[MEX][hapmap]
rs11158655	0.81[GIH][hapmap]
rs12588292	0.81[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs12590065	0.86[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1473732	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1535491	0.81[GIH][hapmap]
rs17104103	0.80[CHD][hapmap]
rs17104114	0.81[CEU][hapmap];0.82[CHD][hapmap];0.80[GIH][hapmap]
rs17104202	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17248526	0.81[GIH][hapmap]
rs1885589	0.80[JPT][hapmap]
rs1885590	0.81[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs2031563	0.80[CHD][hapmap];0.80[GIH][hapmap]
rs2031564	0.88[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2094162	0.86[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2146229	0.81[GIH][hapmap]
rs2146230	0.81[GIH][hapmap]
rs2148160	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2296560	0.83[GIH][hapmap]
rs2296561	0.95[CHB][hapmap];0.86[JPT][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2296562	0.90[ASN][1000 genomes]
rs2296563	0.91[ASN][1000 genomes]
rs2319777	0.82[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28521373	0.81[ASN][1000 genomes]
rs3759755	0.80[CHD][hapmap];0.83[GIH][hapmap]
rs3784085	0.86[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs3818467	0.80[CHD][hapmap];0.81[GIH][hapmap]
rs3818468	0.81[GIH][hapmap]
rs3844530	0.82[ASN][1000 genomes]
rs4636843	0.95[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs57154550	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs58257525	0.93[ASN][1000 genomes]
rs60505324	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6573760	0.81[CHB][hapmap];0.80[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap]
rs6573765	0.91[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs6573768	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6573769	0.86[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs6573770	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs66851210	0.93[ASN][1000 genomes]
rs67968914	0.95[ASN][1000 genomes]
rs68002629	0.89[ASN][1000 genomes]
rs7152903	0.81[GIH][hapmap]
rs7153725	0.81[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs7154607	0.81[CHB][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];0.87[ASN][1000 genomes]
rs7156441	0.80[CHD][hapmap];0.83[GIH][hapmap]
rs7157704	0.88[ASN][1000 genomes]
rs73280987	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs73282707	0.87[ASN][1000 genomes]
rs73284892	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs764039	0.83[CHB][hapmap]
rs8003327	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8004148	0.80[CHD][hapmap];0.80[GIH][hapmap]
rs8004332	0.81[GIH][hapmap]
rs8004488	0.81[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap]
rs8005756	0.88[ASN][1000 genomes]
rs8005876	0.81[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs8006042	0.81[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs8006519	0.84[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap]
rs8007033	0.83[GIH][hapmap]
rs8007696	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs8007866	0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs8008443	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs8008619	0.80[CHD][hapmap];0.83[GIH][hapmap]
rs8008724	0.80[CHD][hapmap];0.83[GIH][hapmap]
rs8015641	0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs8015819	0.90[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs8016024	0.86[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs8016037	0.81[GIH][hapmap]
rs8019109	0.85[ASN][1000 genomes]
rs8020850	0.86[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs8021896	0.81[GIH][hapmap]
rs8021992	0.82[EUR][1000 genomes]
rs9323497	0.86[CHD][hapmap];0.93[GIH][hapmap];0.80[AMR][1000 genomes]
rs960797	0.81[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs9743912	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap]
rs9743983	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]

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	esv2751285	chr14:67364747-67886781	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv1045518	chr14:67529049-67959582	Strong transcription Bivalent Enhancer Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv456331	chr14:67732861-68103780	Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv564961	chr14:67732861-68103780	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers 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	41 gene(s)	inside rSNPs	diseases
5	nsv470651	chr14:67732861-68113293	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
6	nsv1054389	chr14:67804987-67922598	Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
7	nsv542121	chr14:67804987-67922598	Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12588458	ATP6V1D	cis	Thyroid	GTEx
rs12588458	EIF2S1	Cis_1M	lymphoblastoid	RTeQTL
rs12588458	PLEK2	cis	lung	GTEx
rs12588458	EIF2S1	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:67827800-67831400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr14:67827800-67831400	Weak transcription	Left Ventricle	heart
3	chr14:67827800-67831400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr14:67827800-67831600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr14:67827800-67831800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr14:67827800-67832800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr14:67827800-67833600	Weak transcription	Lung	lung
8	chr14:67827800-67834000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr14:67827800-67834000	Weak transcription	Gastric	stomach
10	chr14:67827800-67834800	Weak transcription	Esophagus	oesophagus
11	chr14:67828000-67832000	Weak transcription	Colonic Mucosa	Colon
12	chr14:67828200-67831400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr14:67828200-67831400	Weak transcription	Fetal Muscle Leg	muscle
14	chr14:67828200-67831600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr14:67828200-67831600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr14:67828200-67833600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr14:67828200-67841600	Weak transcription	Aorta	Aorta
18	chr14:67828400-67831000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr14:67828400-67831200	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr14:67828400-67831400	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr14:67828400-67831400	Weak transcription	HSMMtube	muscle
22	chr14:67828400-67831600	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr14:67828400-67831800	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr14:67828400-67832000	Weak transcription	Stomach Smooth Muscle	stomach
25	chr14:67828400-67832200	Weak transcription	Thymus	Thymus
26	chr14:67828400-67832800	Weak transcription	Fetal Intestine Small	intestine
27	chr14:67828400-67837800	Weak transcription	Right Ventricle	heart
28	chr14:67828400-67854000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr14:67828600-67831000	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr14:67828600-67831200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr14:67828600-67831400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr14:67828600-67831400	Weak transcription	NHLF	lung
33	chr14:67828600-67831600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr14:67828600-67832000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr14:67828600-67832000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr14:67828600-67832600	Weak transcription	Fetal Kidney	kidney
37	chr14:67828600-67832800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr14:67828600-67832800	Weak transcription	Fetal Stomach	stomach
39	chr14:67828600-67838000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr14:67828600-67854600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr14:67828800-67831000	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr14:67828800-67832200	Weak transcription	Primary B cells from cord blood	blood
43	chr14:67828800-67832200	Weak transcription	Rectal Smooth Muscle	rectum
44	chr14:67828800-67854000	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr14:67829000-67831800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr14:67829000-67832000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr14:67829000-67832000	Weak transcription	Colon Smooth Muscle	Colon
48	chr14:67829000-67855200	Strong transcription	Fetal Thymus	thymus
49	chr14:67829200-67831200	Genic enhancers	Primary T cells from cord blood	blood
50	chr14:67829200-67836400	Strong transcription	NH-A	brain

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