Variant report

Variant	rs576184
Chromosome Location	chr13:96710538-96710539
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr13:96710062-96710698	A549	lung:	n/a	n/a
2	TEAD4	chr13:96710115-96710564	ECC-1	luminal epithelium:	n/a	n/a
3	CBX3	chr13:96710079-96710563	HCT-116	colon:	n/a	n/a
4	TEAD4	chr13:96710086-96710671	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr13:96710400-96710550	HFF-Myc	foreskin:	n/a	n/a
6	CTCF	chr13:96710089-96710555	HCT-116	colon:	n/a	n/a
7	POLR2A	chr13:96709754-96711049	K562	blood:	n/a	n/a
8	TEAD4	chr13:96710143-96710579	HCT-116	colon:	n/a	n/a
9	TEAD4	chr13:96710077-96710573	ECC-1	luminal epithelium:	n/a	n/a
10	TEAD4	chr13:96710089-96710545	HCT-116	colon:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:96704367..96706595-chr13:96710468..96713623,3	MCF-7	breast:
2	chr13:96704511..96706638-chr13:96708531..96711999,4	MCF-7	breast:
3	chr13:96704058..96705666-chr13:96708973..96710836,2	K562	blood:

No data

Variant related genes	Relation type
UGGT2	TF binding region
ENSG00000102595	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1807900	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1980942	0.82[ASW][hapmap];0.81[YRI][hapmap]
rs1996054	0.80[CEU][hapmap]
rs2389530	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs2774113	0.88[CEU][hapmap]
rs34482628	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs472788	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs473930	0.87[CEU][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4773930	0.81[YRI][hapmap]
rs481927	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs485648	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs489179	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs493109	0.87[CEU][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs506474	0.84[EUR][1000 genomes]
rs509572	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs511029	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs517173	0.85[EUR][1000 genomes]
rs521235	0.88[CEU][hapmap];0.81[YRI][hapmap];0.81[EUR][1000 genomes]
rs527096	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs527680	0.88[CEU][hapmap]
rs529306	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs531090	0.84[EUR][1000 genomes]
rs532399	0.84[EUR][1000 genomes]
rs535812	0.88[EUR][1000 genomes]
rs536606	0.84[EUR][1000 genomes]
rs539604	0.86[CEU][hapmap];0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs541811	0.90[ASW][hapmap];0.88[CEU][hapmap];0.86[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs544080	0.87[CEU][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs551457	0.82[EUR][1000 genomes]
rs552598	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs555221	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs561996	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs590758	0.80[EUR][1000 genomes]
rs592205	0.84[EUR][1000 genomes]
rs595696	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6492826	0.88[CEU][hapmap];0.81[YRI][hapmap]
rs7333045	0.81[YRI][hapmap]
rs7994626	0.94[CHB][hapmap];1.00[YRI][hapmap]
rs7998903	0.84[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs816139	0.82[ASW][hapmap];0.85[YRI][hapmap]
rs9516620	0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9516629	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9525085	0.90[ASW][hapmap];0.80[CEU][hapmap];0.81[YRI][hapmap]
rs9525091	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9525095	0.82[ASW][hapmap];0.80[CEU][hapmap];0.81[YRI][hapmap]
rs9525098	0.85[CEU][hapmap]
rs9525135	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050430	chr13:96508530-97020734	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv541883	chr13:96508530-97020734	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1041165	chr13:96522021-96966520	Enhancers Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1051574	chr13:96550653-96779248	Strong transcription Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1040320	chr13:96573646-96790859	Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv869471	chr13:96622327-97223956	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
7	nsv530390	chr13:96681439-97193029	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
8	nsv900936	chr13:96697209-97032483	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs576184	UGGT2	cis	Muscle Skeletal	GTEx
rs576184	UGCGL2	Cis_1M	lymphoblastoid	RTeQTL
rs576184	DZIP1	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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