Variant report

Variant	rs12587155
Chromosome Location	chr14:78229989-78229990
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	chr14:78223413..78230716-chr14:78265065..78269735,15	MCF-7	breast:
2	chr14:78225717..78227379-chr14:78229569..78231162,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000063761	Chromatin interaction
ENSG00000197734	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1008989	0.91[CHB][hapmap]
rs10483885	0.81[CEU][hapmap]
rs1076496	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs11159294	0.83[MEX][hapmap]
rs12432030	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12587584	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12587825	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12590320	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12880300	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12880840	0.94[ASN][1000 genomes]
rs12881898	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12886631	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12889788	0.86[CHB][hapmap]
rs12891621	0.86[AMR][1000 genomes]
rs12892669	0.86[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.92[MEX][hapmap];0.94[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1477264	0.81[CEU][hapmap]
rs2080816	0.83[MEX][hapmap]
rs2267755	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2267757	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2270443	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2299931	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs35261431	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35657726	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4540996	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4899673	0.81[CEU][hapmap]
rs4899676	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4903624	0.96[CEU][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes]
rs4903644	0.94[ASN][1000 genomes]
rs67408612	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7145979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs726538	0.83[MEX][hapmap]
rs72688831	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8003389	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8003715	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8022886	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758362	chr14:78074180-78262572	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	esv2759998	chr14:78074180-78262572	Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1043788	chr14:78178490-78381190	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS 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 miRNA target site	14 gene(s)	inside rSNPs	diseases
4	esv2754594	chr14:78222798-78275549	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12587155	ADCK1	cis	lymphoblastoid	seeQTL
rs12587155	RPS6KL1	cis	cerebellum	SCAN
rs12587155	SPTLC2	cis	cerebellum	SCAN
rs12587155	ADCK1	cis	multi-tissue	Pritchard

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78228200-78230600	Enhancers	iPS-18 Cell Line	embryonic stem cell
2	chr14:78228200-78230600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr14:78228200-78230800	Weak transcription	Right Ventricle	heart
4	chr14:78228200-78233200	Weak transcription	Fetal Brain Male	brain
5	chr14:78228400-78230400	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr14:78228400-78230600	Enhancers	H1 Cell Line	embryonic stem cell
7	chr14:78228400-78230800	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr14:78228400-78231000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr14:78228400-78234800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr14:78228600-78230600	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr14:78229600-78230000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr14:78229600-78230000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr14:78229600-78230400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr14:78229600-78230600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr14:78229600-78230800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr14:78229800-78230200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr14:78229800-78230200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr14:78229800-78230200	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr14:78229800-78230400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr14:78229800-78230800	Enhancers	Brain Germinal Matrix	brain

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