Variant report

Variant	rs12890828
Chromosome Location	chr14:78229185-78229186
allele	C/T
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	chr14:78173969..78175847-chr14:78226797..78229509,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119705	Chromatin interaction
ENSG00000063761	Chromatin interaction
ENSG00000100601	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10134425	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10138747	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10139492	0.82[ASN][1000 genomes]
rs10143294	0.82[ASN][1000 genomes]
rs10144448	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10146255	0.92[ASN][1000 genomes]
rs10483885	0.84[ASN][1000 genomes]
rs114763	0.87[ASN][1000 genomes]
rs11846215	0.86[ASN][1000 genomes]
rs12879880	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12887313	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1477263	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1477264	0.93[ASN][1000 genomes]
rs176941	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs176947	0.81[ASN][1000 genomes]
rs176948	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs176954	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs176956	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs176959	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs176961	0.87[ASN][1000 genomes]
rs176963	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs176964	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs176965	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs176968	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs176969	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs176970	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs176972	0.86[ASN][1000 genomes]
rs176975	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs176976	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs176977	0.86[ASN][1000 genomes]
rs2080703	0.82[ASN][1000 genomes]
rs2267756	0.82[ASN][1000 genomes]
rs2267762	0.81[ASN][1000 genomes]
rs2267763	0.82[ASN][1000 genomes]
rs2267764	0.82[ASN][1000 genomes]
rs2267766	0.81[AMR][1000 genomes]
rs2277917	0.93[ASN][1000 genomes]
rs2284233	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2284234	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2284235	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3783981	0.82[ASN][1000 genomes]
rs3783982	0.82[ASN][1000 genomes]
rs4641655	0.92[ASN][1000 genomes]
rs4899670	0.82[ASN][1000 genomes]
rs4899673	0.84[ASN][1000 genomes]
rs4899674	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4903638	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6574392	0.90[ASN][1000 genomes]
rs6574394	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6574399	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7143926	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7145717	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7148078	0.92[ASN][1000 genomes]
rs7148126	0.82[ASN][1000 genomes]
rs7150531	0.91[ASN][1000 genomes]
rs7151685	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7154571	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7159310	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7160355	0.90[ASN][1000 genomes]
rs717682	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs759713	0.82[ASN][1000 genomes]
rs8010541	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8015645	0.81[ASN][1000 genomes]
rs8022516	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9323649	0.82[ASN][1000 genomes]
rs9323651	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78228000-78229800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr14:78228200-78230600	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr14:78228200-78230600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr14:78228200-78230800	Weak transcription	Right Ventricle	heart
5	chr14:78228200-78233200	Weak transcription	Fetal Brain Male	brain
6	chr14:78228400-78229600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr14:78228400-78229600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr14:78228400-78229600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr14:78228400-78229600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr14:78228400-78229600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr14:78228400-78229800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr14:78228400-78229800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr14:78228400-78229800	Weak transcription	Brain Germinal Matrix	brain
14	chr14:78228400-78230400	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr14:78228400-78230600	Enhancers	H1 Cell Line	embryonic stem cell
16	chr14:78228400-78230800	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr14:78228400-78231000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr14:78228400-78234800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr14:78228600-78229800	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr14:78228600-78230600	Enhancers	HUES64 Cell Line	embryonic stem cell

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