Variant report

Variant	rs12436172
Chromosome Location	chr14:69950865-69950866
allele	A/C
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	GATA3	chr14:69950556-69950878	T-47D	breast:	n/a	n/a
2	ZBTB7A	chr14:69950544-69951924	ECC-1	luminal epithelium:	n/a	chr14:69951500-69951509
3	TEAD4	chr14:69950721-69951295	H1-hESC	embryonic stem cell:	n/a	n/a
4	TEAD4	chr14:69950805-69951265	H1-hESC	embryonic stem cell:	n/a	n/a
5	ESR1	chr14:69950262-69950928	ECC-1	luminal epithelium:	n/a	n/a
6	MAX	chr14:69950865-69951399	H1-hESC	embryonic stem cell:	n/a	n/a
7	MAX	chr14:69950230-69951884	ECC-1	luminal epithelium:	n/a	n/a
8	ESR1	chr14:69950322-69950903	ECC-1	luminal epithelium:	n/a	n/a
9	ZBTB7A	chr14:69950355-69952126	ECC-1	luminal epithelium:	n/a	chr14:69950517-69950526 chr14:69951500-69951509
10	NFIC	chr14:69950115-69951327	ECC-1	luminal epithelium:	n/a	n/a
11	TAF1	chr14:69950372-69951792	ECC-1	luminal epithelium:	n/a	n/a
12	ESR1	chr14:69950314-69951024	ECC-1	luminal epithelium:	n/a	n/a
13	CTBP2	chr14:69950474-69951751	H1-hESC	embryonic stem cell:	n/a	n/a
14	TEAD4	chr14:69950247-69951637	ECC-1	luminal epithelium:	n/a	n/a
15	NR2F2	chr14:69950492-69952129	MCF-7	breast:	n/a	n/a
16	TCF12	chr14:69950148-69951705	ECC-1	luminal epithelium:	n/a	chr14:69951023-69951031
17	POLR2A	chr14:69950357-69951674	ECC-1	luminal epithelium:	n/a	n/a
18	SIN3A	chr14:69950441-69951712	H1-hESC	embryonic stem cell:	n/a	chr14:69951658-69951671 chr14:69951364-69951377 chr14:69950533-69950546
19	POLR2A	chr14:69950576-69950905	H1-neurons	neurons:	n/a	n/a
20	HDAC2	chr14:69950359-69951785	MCF-7	breast:	n/a	n/a
21	MAX	chr14:69950187-69951692	ECC-1	luminal epithelium:	n/a	n/a
22	YY1	chr14:69950441-69950899	ECC-1	luminal epithelium:	n/a	chr14:69950812-69950821 chr14:69950816-69950827 chr14:69950675-69950689 chr14:69950815-69950824 chr14:69950813-69950824
23	BACH1	chr14:69950648-69951056	H1-hESC	embryonic stem cell:	n/a	n/a
24	CEBPB	chr14:69950226-69950924	ECC-1	luminal epithelium:	n/a	n/a
25	MAX	chr14:69950476-69951987	MCF-7	breast:	n/a	n/a
26	TEAD4	chr14:69950247-69951558	ECC-1	luminal epithelium:	n/a	n/a
27	TCF12	chr14:69950177-69951768	ECC-1	luminal epithelium:	n/a	chr14:69951023-69951031
28	HDAC2	chr14:69950530-69951309	MCF-7	breast:	n/a	n/a
29	EP300	chr14:69950338-69951140	ECC-1	luminal epithelium:	n/a	chr14:69950814-69950823
30	GABPA	chr14:69950401-69951292	MCF-7	breast:	n/a	chr14:69951187-69951196 chr14:69951282-69951291
31	EP300	chr14:69950137-69951706	ECC-1	luminal epithelium:	n/a	chr14:69951282-69951291 chr14:69950814-69950823 chr14:69951543-69951559
32	ELF1	chr14:69950424-69951973	MCF-7	breast:	n/a	chr14:69951225-69951237 chr14:69951656-69951668 chr14:69950813-69950825 chr14:69950812-69950821 chr14:69950815-69950824
33	TAF1	chr14:69950807-69951664	ECC-1	luminal epithelium:	n/a	n/a
34	E2F6	chr14:69950615-69951619	H1-hESC	embryonic stem cell:	n/a	chr14:69951340-69951349 chr14:69950813-69950823
35	FOXM1	chr14:69950246-69951225	ECC-1	luminal epithelium:	n/a	n/a
36	NFIC	chr14:69950182-69951608	ECC-1	luminal epithelium:	n/a	n/a
37	E2F6	chr14:69950805-69951967	H1-hESC	embryonic stem cell:	n/a	chr14:69951340-69951349 chr14:69950813-69950823
38	MAX	chr14:69950369-69951928	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr14:69950411-69951334	ECC-1	luminal epithelium:	n/a	n/a
40	HA-E2F1	chr14:69950256-69951777	MCF-7	breast:	n/a	chr14:69951340-69951349 chr14:69950813-69950823
41	GABPA	chr14:69950523-69951033	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:69862767..69865090-chr14:69948473..69950881,2	MCF-7	breast:
2	chr14:69946123..69947705-chr14:69948349..69951147,2	MCF-7	breast:
3	chr14:69950456..69952040-chr14:70233397..70235258,2	MCF-7	breast:
4	chr14:69947861..69950985-chr14:69958572..69961159,3	MCF-7	breast:
5	chr14:69949714..69952374-chr14:70039182..70041131,3	MCF-7	breast:
6	chr14:69949476..69951469-chr14:70232962..70234565,2	MCF-7	breast:

Variant related genes	Relation type
PLEKHD1	TF binding region
ENSG00000100632	Chromatin interaction
ENSG00000029364	Chromatin interaction
ENSG00000100650	Chromatin interaction
ENSG00000267909	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10129720	0.89[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10151691	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11623094	0.84[CEU][hapmap];0.89[CHB][hapmap];0.95[YRI][hapmap]
rs12147478	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12147967	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1466255	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1965878	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2100489	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2124192	0.92[CEU][hapmap];0.89[CHB][hapmap]
rs34405286	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3759770	0.84[CEU][hapmap];0.89[CHB][hapmap];0.91[YRI][hapmap]
rs4902719	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56392460	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7150586	0.89[CHB][hapmap];0.95[YRI][hapmap]
rs7160248	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8010767	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9796392	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3396933	chr14:69906914-70001258	Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1048882	chr14:69920881-69976694	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1052107	chr14:69922552-69969297	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1039230	chr14:69922552-69972002	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1039192	chr14:69922552-69976694	Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv456335	chr14:69928307-69971598	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv564967	chr14:69928307-69971598	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv1050258	chr14:69942127-69976694	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
9	esv3357015	chr14:69950224-69952772	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12436172	SLC39A9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:69949800-69952600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr14:69950400-69951000	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr14:69950400-69951200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr14:69950400-69951200	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
5	chr14:69950400-69951200	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
6	chr14:69950400-69951200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
7	chr14:69950400-69951200	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
8	chr14:69950400-69951400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
9	chr14:69950400-69951400	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
10	chr14:69950400-69951600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
11	chr14:69950400-69951600	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
12	chr14:69950400-69951600	Flanking Bivalent TSS/Enh	Ovary	ovary
13	chr14:69950400-69951800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
14	chr14:69950400-69951800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
15	chr14:69950400-69951800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr14:69950400-69951800	Bivalent/Poised TSS	Brain Angular Gyrus	brain
17	chr14:69950400-69951800	Bivalent Enhancer	Fetal Brain Male	brain
18	chr14:69950400-69952000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
19	chr14:69950400-69952000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
20	chr14:69950400-69952000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr14:69950400-69952000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
22	chr14:69950400-69952000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
23	chr14:69950400-69952000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
24	chr14:69950400-69952000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr14:69950400-69952000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr14:69950400-69952000	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
27	chr14:69950400-69952200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
28	chr14:69950400-69952200	Bivalent Enhancer	Spleen	Spleen
29	chr14:69950600-69951000	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr14:69950600-69951000	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr14:69950600-69951000	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr14:69950600-69951000	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
33	chr14:69950600-69951000	Enhancers	Aorta	Aorta
34	chr14:69950600-69951000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
35	chr14:69950600-69951000	Bivalent/Poised TSS	Fetal Kidney	kidney
36	chr14:69950600-69951000	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr14:69950600-69951000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
38	chr14:69950600-69951000	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
39	chr14:69950600-69951000	Bivalent Enhancer	HUVEC	blood vessel
40	chr14:69950600-69951200	Flanking Bivalent TSS/Enh	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr14:69950600-69951200	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
42	chr14:69950600-69951200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
43	chr14:69950600-69951200	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
44	chr14:69950600-69951200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
45	chr14:69950600-69951200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
46	chr14:69950600-69951200	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
47	chr14:69950600-69951200	Flanking Active TSS	Pancreas	Pancrea
48	chr14:69950600-69951200	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
49	chr14:69950600-69951200	Flanking Active TSS	Right Ventricle	heart
50	chr14:69950600-69951200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links