Variant report

Variant	rs12894700
Chromosome Location	chr14:56007846-56007847
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	POLR2A	chr14:56007841-56008230	SK-N-SH	brain:	n/a	n/a
2	EP300	chr14:56006091-56009536	SK-N-SH	brain:	n/a	n/a
3	JUND	chr14:56007788-56008290	SK-N-SH	brain:	n/a	chr14:56008213-56008222 chr14:56008059-56008070
4	NR2F2	chr14:56007574-56008389	MCF-7	breast:	n/a	n/a
5	NFIC	chr14:56007717-56008384	SK-N-SH	brain:	n/a	n/a
6	JUND	chr14:56007764-56008424	SK-N-SH	brain:	n/a	chr14:56008213-56008222 chr14:56008059-56008070
7	MXI1	chr14:56006094-56007850	SK-N-SH	brain:	n/a	n/a
8	JUND	chr14:56007700-56008462	T-47D	breast:	n/a	chr14:56008213-56008222 chr14:56008059-56008070
9	HDAC2	chr14:56007675-56008423	MCF-7	breast:	n/a	chr14:56008379-56008393
10	GATA3	chr14:56007523-56008547	SK-N-SH	brain:	n/a	n/a
11	EP300	chr14:56007838-56008301	SK-N-SH	brain:	n/a	n/a
12	STAT3	chr14:56007508-56008339	MCF10A-Er-Src	breast:	n/a	n/a
13	FOS	chr14:56007825-56008275	HUVEC	blood vessel:	n/a	chr14:56008213-56008222 chr14:56008059-56008070
14	EP300	chr14:56007772-56008437	MCF-7	breast:	n/a	n/a
15	EP300	chr14:56007674-56008457	T-47D	breast:	n/a	n/a
16	FOSL2	chr14:56007727-56008345	MCF-7	breast:	n/a	chr14:56008213-56008222
17	JUND	chr14:56007730-56008416	T-47D	breast:	n/a	chr14:56008213-56008222 chr14:56008059-56008070
18	GATA3	chr14:56007714-56008308	MCF-7	breast:	n/a	n/a
19	GATA3	chr14:56007739-56008502	A549	lung:	n/a	n/a
20	FOXM1	chr14:56007470-56008423	MCF-7	breast:	n/a	n/a
21	GATA2	chr14:56007620-56008324	HUVEC	blood vessel:	n/a	n/a
22	PBX3	chr14:56007786-56008345	SK-N-SH	brain:	n/a	n/a
23	JUND	chr14:56007677-56008416	MCF-7	breast:	n/a	chr14:56008213-56008222 chr14:56008059-56008070
24	NR2F2	chr14:56007221-56008462	MCF-7	breast:	n/a	n/a
25	TCF12	chr14:56007657-56008441	SK-N-SH	brain:	n/a	n/a
26	SIN3AK20	chr14:56007390-56008546	MCF-7	breast:	n/a	n/a
27	FOXM1	chr14:56007784-56008340	MCF-7	breast:	n/a	n/a
28	ESR1	chr14:56007817-56008273	T-47D	breast:	n/a	n/a
29	FOSL2	chr14:56007778-56008350	SK-N-SH	brain:	n/a	chr14:56008213-56008222
30	GATA3	chr14:56007271-56008502	MCF-7	breast:	n/a	n/a
31	EP300	chr14:56007775-56008362	MCF-7	breast:	n/a	n/a
32	FOXA1	chr14:56007816-56008363	T-47D	breast:	n/a	n/a
33	TCF12	chr14:56007665-56008392	SK-N-SH	brain:	n/a	n/a
34	GATA3	chr14:56007568-56008131	SH-SY5Y	brain:	n/a	n/a
35	TCF7L2	chr14:56007640-56008184	MCF-7	breast:	n/a	n/a
36	SIN3AK20	chr14:56007392-56008480	MCF-7	breast:	n/a	n/a
37	CEBPB	chr14:56007451-56008509	MCF-7	breast:	n/a	n/a
38	ZNF217	chr14:56007641-56008447	MCF-7	breast:	n/a	n/a
39	PBX3	chr14:56007831-56008426	SK-N-SH	brain:	n/a	n/a
40	GATA3	chr14:56006902-56008405	MCF-7	breast:	n/a	n/a
41	FOSL2	chr14:56007673-56008371	MCF-7	breast:	n/a	chr14:56008213-56008222
42	RFX5	chr14:56007840-56008311	Hela-S3	cervix:	n/a	n/a
43	TCF12	chr14:56007584-56008401	MCF-7	breast:	n/a	n/a
44	GATA3	chr14:56007307-56008678	MCF-7	breast:	n/a	n/a
45	FOSL2	chr14:56007780-56008290	A549	lung:	n/a	chr14:56008213-56008222
46	GATA3	chr14:56007625-56008460	SK-N-SH	brain:	n/a	n/a
47	GATA3	chr14:56007691-56008363	T-47D	breast:	n/a	n/a
48	JUND	chr14:56007634-56008379	MCF-7	breast:	n/a	chr14:56008213-56008222 chr14:56008059-56008070
49	GATA3	chr14:56007654-56008441	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:55913599..55916759-chr14:56004997..56009666,4	MCF-7	breast:

Variant related genes	Relation type
RPL7AP4	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11847588	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs11847813	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12886742	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12890794	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12890934	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17128552	1.00[ASW][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs17128557	0.97[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1951892	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1951893	1.00[CEU][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2181742	0.86[ASN][1000 genomes]
rs2181743	0.86[ASN][1000 genomes]
rs2341884	0.81[JPT][hapmap];0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs3825617	0.90[ASN][1000 genomes]
rs4143891	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4898867	0.82[EUR][1000 genomes]
rs4898868	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4901578	0.86[ASN][1000 genomes]
rs4901579	0.86[ASN][1000 genomes]
rs4901580	0.86[ASN][1000 genomes]
rs4901581	0.84[ASN][1000 genomes]
rs4901582	0.86[ASN][1000 genomes]
rs4901584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4901586	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55823239	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6573037	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6573038	0.91[CEU][hapmap]
rs6573040	0.83[ASN][1000 genomes]
rs8010372	0.82[EUR][1000 genomes]
rs8017185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9796397	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv901958	chr14:55822095-56045411	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv901960	chr14:55853724-56085130	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv901961	chr14:55853724-56101879	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv901962	chr14:55862956-56101879	Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv901963	chr14:55871452-56085130	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv901964	chr14:55871452-56101879	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
7	nsv564874	chr14:55879685-56027815	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv1051564	chr14:55895610-56130788	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv542103	chr14:55895610-56130788	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
10	nsv1047054	chr14:55922287-56035579	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv1037161	chr14:55928030-56039353	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv901965	chr14:55976428-56101879	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12894700	WDHD1	cis	cerebellum	SCAN
rs12894700	KTN1	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55999800-56020400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr14:56001000-56009400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr14:56006000-56010200	Weak transcription	HSMMtube	muscle
4	chr14:56006200-56009000	Enhancers	Hela-S3	cervix
5	chr14:56006400-56008200	Enhancers	Stomach Mucosa	stomach
6	chr14:56006400-56008400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr14:56006800-56009000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr14:56007200-56010000	Weak transcription	Fetal Heart	heart
9	chr14:56007400-56008600	Enhancers	HMEC	breast
10	chr14:56007400-56008600	Enhancers	HUVEC	blood vessel
11	chr14:56007400-56009000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr14:56007600-56008400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr14:56007600-56008400	Flanking Active TSS	A549	lung
14	chr14:56007600-56008600	Enhancers	Pancreatic Islets	Pancreatic Islet
15	chr14:56007600-56008800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr14:56007600-56009400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr14:56007600-56010400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr14:56007800-56008200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr14:56007800-56008600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr14:56007800-56008600	Enhancers	NHEK	skin
21	chr14:56007800-56008800	Enhancers	NH-A	brain
22	chr14:56007800-56010400	Enhancers	Muscle Satellite Cultured Cells	--

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