Variant report

Variant	rs12878589
Chromosome Location	chr14:105050924-105050925
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	chr14:105048877..105053029-chr14:105053228..105056172,3	MCF-7	breast:
2	chr14:104652967..104655075-chr14:105050050..105051684,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10132112	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12589619	1.00[CEU][hapmap]
rs12878336	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12880814	0.83[ASN][1000 genomes]
rs12884743	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12888830	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34024274	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34058091	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35246301	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3809457	0.82[YRI][hapmap]
rs4077167	0.83[ASN][1000 genomes]
rs4270105	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4454893	0.82[YRI][hapmap]
rs4983500	1.00[CEU][hapmap]
rs7142224	0.82[YRI][hapmap]
rs7151177	1.00[CEU][hapmap]
rs9788432	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9788527	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.83[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1826669	chr14:104554461-105065941	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1049810	chr14:104577600-105060539	Bivalent Enhancer Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv530812	chr14:104775571-105364883	Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS 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	98 gene(s)	inside rSNPs	diseases
4	esv2761599	chr14:104789113-105067734	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1042527	chr14:104968968-105052401	Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv542222	chr14:104968968-105052401	Bivalent Enhancer Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1051647	chr14:104983302-105153720	Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
8	nsv542223	chr14:104983302-105153720	Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
9	esv1816766	chr14:105007585-105126354	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv902371	chr14:105011436-105057102	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv902372	chr14:105011436-105200377	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
12	nsv902373	chr14:105012858-105078153	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv470676	chr14:105023512-105100021	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv456445	chr14:105023512-105170003	Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
15	nsv566047	chr14:105023512-105170003	Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
16	nsv1053591	chr14:105024558-105475931	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
17	nsv542224	chr14:105024558-105475931	Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
18	nsv1044032	chr14:105036464-105124567	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
19	nsv902374	chr14:105045524-105119784	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
20	nsv902375	chr14:105045524-105139894	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
21	esv3355179	chr14:105048007-105052305	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:105038000-105051000	Enhancers	Fetal Intestine Large	intestine
2	chr14:105041000-105051200	Enhancers	Fetal Intestine Small	intestine
3	chr14:105044800-105053600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr14:105045600-105053200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr14:105046400-105064000	Weak transcription	Brain Anterior Caudate	brain
6	chr14:105048000-105052000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr14:105048000-105053400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr14:105048200-105053600	Weak transcription	Brain Angular Gyrus	brain
9	chr14:105048400-105051000	Bivalent Enhancer	Fetal Stomach	stomach
10	chr14:105048400-105051800	Enhancers	K562	blood
11	chr14:105048800-105051600	Enhancers	Placenta Amnion	Placenta Amnion
12	chr14:105049200-105054800	Enhancers	Fetal Muscle Leg	muscle
13	chr14:105049200-105057400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
14	chr14:105049200-105057400	Bivalent Enhancer	Placenta	Placenta
15	chr14:105049600-105054200	Enhancers	Left Ventricle	heart
16	chr14:105049800-105052400	Enhancers	Right Atrium	heart
17	chr14:105050000-105051000	Genic enhancers	Right Ventricle	heart
18	chr14:105050000-105053800	Weak transcription	Gastric	stomach
19	chr14:105050200-105054800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
20	chr14:105050400-105051000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr14:105050400-105051200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr14:105050400-105051200	Enhancers	Fetal Brain Male	brain
23	chr14:105050400-105054200	Enhancers	Adipose Nuclei	Adipose
24	chr14:105050400-105055000	Enhancers	Fetal Heart	heart
25	chr14:105050600-105053200	Weak transcription	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links