Variant report

Variant	rs1008988
Chromosome Location	chr14:78260795-78260796
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	chr14:78173247..78175139-chr14:78259767..78262393,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100601	Chromatin interaction
ENSG00000119705	Chromatin interaction

Extended variants
information (count: 125 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs1006038	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1006039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1006040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10136053	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10139492	0.95[CHB][hapmap]
rs10142722	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10143294	0.95[CHB][hapmap]
rs10144448	0.95[CHB][hapmap]
rs10148373	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10149619	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1048147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10483885	0.95[CHB][hapmap]
rs11159288	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs114763	0.95[CHB][hapmap]
rs11622565	0.83[ASN][1000 genomes]
rs11623088	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11624101	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11628888	0.92[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap]
rs11847025	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12435761	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12883228	0.86[ASN][1000 genomes]
rs12885306	0.95[CHB][hapmap]
rs12887282	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12887606	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12890375	0.89[ASN][1000 genomes]
rs12890728	0.94[CHB][hapmap];0.87[ASN][1000 genomes]
rs13379065	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1469018	0.89[ASN][1000 genomes]
rs1477259	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1477260	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1477261	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1477262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1477264	0.95[CHB][hapmap]
rs1549119	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17106157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs176941	0.95[CHB][hapmap]
rs176943	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs176944	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs176946	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs176951	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs176952	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs176953	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs176955	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs176956	0.95[CHB][hapmap]
rs176957	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs176959	0.95[CHB][hapmap]
rs176960	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs176962	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs176963	0.95[CHB][hapmap]
rs176964	1.00[CHB][hapmap]
rs176965	0.95[CHB][hapmap]
rs176966	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs176971	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs176973	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs176979	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs176980	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1978416	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1984925	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2032781	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2112136	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2267756	0.95[CHB][hapmap]
rs2267758	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2267759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2267760	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2267761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2267762	0.95[CHB][hapmap]
rs2267763	0.95[CHB][hapmap]
rs2267764	0.95[CHB][hapmap]
rs2267767	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2267768	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2277917	0.95[CHB][hapmap]
rs2284234	0.95[CHB][hapmap]
rs2284235	0.95[CHB][hapmap]
rs2299930	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2364584	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2364840	0.87[ASN][1000 genomes]
rs2544567	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28534379	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28603114	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35204328	0.83[ASN][1000 genomes]
rs3759728	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3783980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3783983	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4383070	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4632066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4635269	0.82[ASN][1000 genomes]
rs4899670	0.95[CHB][hapmap]
rs4899673	0.95[CHB][hapmap]
rs4903643	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55909252	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56017708	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56412551	0.85[ASN][1000 genomes]
rs57635466	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61993668	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6574388	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6574391	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6574399	0.95[CHB][hapmap]
rs6574402	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6574404	0.95[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs7142390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7143926	0.95[CHB][hapmap]
rs7147516	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7148078	0.90[CHB][hapmap]
rs7151211	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7151685	0.95[CHB][hapmap]
rs717683	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72685264	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs759713	0.95[CHB][hapmap]
rs759808	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8003691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8003979	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8011337	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8014635	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8015645	0.95[CHB][hapmap]
rs8016175	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8016447	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8018741	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8018971	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9323649	0.95[CHB][hapmap]
rs9323650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9323651	0.95[CHB][hapmap]

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:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78253600-78260800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr14:78253600-78261800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr14:78253800-78266200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr14:78257400-78262000	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr14:78258000-78261800	Weak transcription	HMEC	breast
6	chr14:78258000-78262000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr14:78258000-78262000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr14:78258000-78262200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr14:78258200-78262000	Weak transcription	Placenta	Placenta
10	chr14:78258200-78262000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr14:78258200-78262000	Weak transcription	HepG2	liver
12	chr14:78258200-78262200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr14:78258200-78262200	Weak transcription	NHEK	skin
14	chr14:78258400-78261800	Weak transcription	Hela-S3	cervix
15	chr14:78259600-78266200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr14:78260600-78260800	Enhancers	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links