Variant report

Variant	rs229701
Chromosome Location	chr14:45237624-45237625
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:45234847..45238441-chr14:45239619..45243336,5	MCF-7	breast:
2	chr14:45230477..45232616-chr14:45235679..45238276,2	MCF-7	breast:
3	chr14:45235346..45237899-chr17:57923729..57925235,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000201524	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs170687	0.93[EUR][1000 genomes]
rs170688	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs170689	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs170690	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs170691	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs17115489	0.95[EUR][1000 genomes]
rs17115496	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17115558	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs179349	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs184529	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs189088	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs192037	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs229683	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs229684	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs229685	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs229686	0.98[EUR][1000 genomes]
rs229687	0.98[EUR][1000 genomes]
rs229688	0.83[EUR][1000 genomes]
rs229689	0.98[EUR][1000 genomes]
rs229690	0.98[EUR][1000 genomes]
rs229692	0.93[EUR][1000 genomes]
rs229693	0.89[EUR][1000 genomes]
rs229694	0.93[EUR][1000 genomes]
rs229695	0.93[EUR][1000 genomes]
rs229696	0.93[EUR][1000 genomes]
rs229698	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs229699	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs229700	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs229702	0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs229703	1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs229704	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs229705	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs229706	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs229707	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs229708	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs229709	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs229710	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs229711	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs229712	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs229713	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs229714	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs229715	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs229716	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs229717	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs229719	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs229720	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs229721	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs229722	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs229724	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs229743	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs229744	0.87[AMR][1000 genomes]
rs371224	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs374976	0.93[EUR][1000 genomes]
rs392584	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs401737	0.93[EUR][1000 genomes]
rs452831	0.93[EUR][1000 genomes]
rs452832	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054134	chr14:44501865-45271806	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv542074	chr14:44501865-45271806	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv869289	chr14:44752382-45447415	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	nsv901832	chr14:44847444-45415597	Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	nsv869391	chr14:44948825-45241392	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv995092	chr14:44973489-45393462	Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
7	nsv901836	chr14:45054777-45283699	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv2758356	chr14:45057833-45313666	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	esv2759986	chr14:45057833-45313666	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv517384	chr14:45060617-45250418	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv901838	chr14:45069249-45297050	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv1039879	chr14:45131989-45244622	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv1050829	chr14:45157388-45318232	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	esv2757566	chr14:45169402-45254884	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
15	nsv1047886	chr14:45189653-45543182	Strong transcription Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
16	nsv542079	chr14:45189653-45543182	Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
17	nsv901841	chr14:45198196-45719643	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
18	nsv1053437	chr14:45232269-45424222	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs229701	RP11-398E10.1	cis	Nerve Tibial	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:45236600-45237800	Enhancers	ES-I3 Cell Line	embryonic stem cell
2	chr14:45236600-45237800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr14:45236600-45238200	Enhancers	Fetal Lung	lung
4	chr14:45236800-45237800	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr14:45236800-45238000	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr14:45236800-45238600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr14:45237000-45237800	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr14:45237000-45237800	Enhancers	Fetal Stomach	stomach
9	chr14:45237000-45238000	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr14:45237000-45238600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr14:45237000-45239600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr14:45237400-45237800	Weak transcription	HUES6 Cell Line	embryonic stem cell

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