Variant report

Variant	rs73427831
Chromosome Location	chr7:120499778-120499779
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr7:120499560-120499904	T-47D	breast:	n/a	n/a
2	GATA3	chr7:120499561-120499843	T-47D	breast:	n/a	n/a
3	FOXA1	chr7:120499643-120499824	T-47D	breast:	n/a	n/a
4	FOXA1	chr7:120499627-120499848	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:120492091..120494339-chr7:120499581..120501405,2	K562	blood:

Variant related genes	Relation type
TSPAN12	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10257297	0.81[ASN][1000 genomes]
rs10257475	0.81[ASN][1000 genomes]
rs10261886	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13438082	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17132716	0.95[ASN][1000 genomes]
rs17143001	0.81[ASN][1000 genomes]
rs17143009	0.81[ASN][1000 genomes]
rs17143055	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2107276	0.88[ASN][1000 genomes]
rs2158323	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2158324	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2189452	0.89[ASN][1000 genomes]
rs2402551	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3757557	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3779386	0.87[ASN][1000 genomes]
rs3779387	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3779388	0.89[ASN][1000 genomes]
rs3779389	0.82[ASN][1000 genomes]
rs4141301	0.85[AMR][1000 genomes]
rs4141309	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4461820	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56755229	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs56922360	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57457261	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57818444	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs58686737	0.89[ASN][1000 genomes]
rs59169713	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59189516	0.85[AMR][1000 genomes]
rs59567952	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59790582	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs60612048	0.85[AMR][1000 genomes]
rs60837162	0.89[ASN][1000 genomes]
rs61043018	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6971854	0.87[ASN][1000 genomes]
rs6975372	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6979247	0.81[ASN][1000 genomes]
rs73427805	0.87[ASN][1000 genomes]
rs73427834	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73427862	0.81[ASN][1000 genomes]
rs73429803	0.81[ASN][1000 genomes]
rs7776721	0.81[ASN][1000 genomes]
rs7779136	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7779149	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7779941	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7780130	0.85[AMR][1000 genomes]
rs7780247	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7780690	0.82[AMR][1000 genomes]
rs7789807	0.92[ASN][1000 genomes]
rs7799562	0.82[AMR][1000 genomes]
rs7800318	0.87[ASN][1000 genomes]
rs7806629	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9648991	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9648992	0.93[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9648993	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9649427	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9649428	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9649429	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1818826	chr7:120405335-120622836	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv5929	chr7:120467591-120513472	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 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	chr7:120498400-120504600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:120498400-120506800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr7:120498600-120499800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr7:120498600-120499800	Weak transcription	Colonic Mucosa	Colon
5	chr7:120498800-120499800	Enhancers	Fetal Heart	heart
6	chr7:120499000-120500200	Enhancers	Fetal Intestine Small	intestine
7	chr7:120499000-120500200	Enhancers	Rectal Mucosa Donor 29	rectum
8	chr7:120499000-120500400	Enhancers	Fetal Intestine Large	intestine
9	chr7:120499000-120503200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr7:120499000-120504600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr7:120499000-120504800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr7:120499200-120499800	Weak transcription	Small Intestine	intestine
13	chr7:120499200-120500000	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr7:120499200-120504400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr7:120499400-120500400	Enhancers	Fetal Muscle Leg	muscle
16	chr7:120499400-120504600	Weak transcription	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links