Variant report

Variant	rs4345139
Chromosome Location	chr4:88162693-88162694
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:24)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:24 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF7L2	chr4:88162495-88162861	PANC-1	pancreas:	n/a	n/a
2	GATA3	chr4:88162359-88162978	MCF-7	breast:	n/a	n/a
3	JUND	chr4:88162401-88162898	MCF-7	breast:	n/a	n/a
4	TCF12	chr4:88162435-88162939	MCF-7	breast:	n/a	n/a
5	NR2F2	chr4:88162472-88163002	MCF-7	breast:	n/a	n/a
6	ZNF217	chr4:88162467-88162830	MCF-7	breast:	n/a	n/a
7	FOXA1	chr4:88162496-88162896	T-47D	breast:	n/a	n/a
8	CTCF	chr4:88162600-88162750	BE2_C	brain:	n/a	n/a
9	GATA3	chr4:88162436-88162912	T-47D	breast:	n/a	n/a
10	HDAC2	chr4:88162388-88162916	MCF-7	breast:	n/a	n/a
11	GATA3	chr4:88162479-88162880	MCF-7	breast:	n/a	n/a
12	GATA3	chr4:88162540-88162864	MCF-7	breast:	n/a	n/a
13	EP300	chr4:88162536-88162906	T-47D	breast:	n/a	n/a
14	SIN3AK20	chr4:88162393-88162945	MCF-7	breast:	n/a	n/a
15	HDAC2	chr4:88162486-88162950	MCF-7	breast:	n/a	n/a
16	FOXM1	chr4:88162442-88163127	MCF-7	breast:	n/a	n/a
17	GATA3	chr4:88162214-88163212	MCF-7	breast:	n/a	n/a
18	FOXA1	chr4:88162509-88162862	T-47D	breast:	n/a	n/a
19	SIN3AK20	chr4:88162263-88163130	MCF-7	breast:	n/a	n/a
20	EP300	chr4:88162474-88162900	MCF-7	breast:	n/a	n/a
21	GATA3	chr4:88162435-88162910	T-47D	breast:	n/a	n/a
22	CCNT2	chr4:88162651-88162835	K562	blood:	n/a	n/a
23	EP300	chr4:88162549-88162827	T-47D	breast:	n/a	n/a
24	NR2F2	chr4:88162472-88162961	MCF-7	breast:	n/a	n/a

No data

Variant related genes	Relation type
KLHL8	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10084835	0.83[YRI][hapmap]
rs11097130	0.90[JPT][hapmap]
rs12649023	0.81[CHB][hapmap]
rs13108668	0.83[LWK][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes]
rs13112695	0.81[CHB][hapmap];0.83[CHD][hapmap]
rs13149842	0.90[ASN][1000 genomes]
rs3923441	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.82[MEX][hapmap];0.91[MKK][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs3923442	0.83[YRI][hapmap]
rs4331742	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4352444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6531975	0.81[CHB][hapmap];0.83[CHD][hapmap]
rs6531977	0.81[CHB][hapmap]
rs6816742	0.83[YRI][hapmap]
rs7668929	0.81[YRI][hapmap]
rs7672465	0.92[ASN][1000 genomes]
rs7688962	0.81[CHB][hapmap]
rs7692397	0.94[YRI][hapmap]
rs7699556	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997750	chr4:87933945-88264127	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1007020	chr4:88046263-88235018	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv537169	chr4:88046263-88235018	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv1014846	chr4:88151614-88188335	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv537170	chr4:88151614-88188335	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4345139	PKD2	cis	parietal	SCAN
rs4345139	PPM1K	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88160400-88162800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr4:88161600-88163200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr4:88161800-88162800	Enhancers	A549	lung
4	chr4:88162600-88162800	ZNF genes & repeats	Small Intestine	intestine
5	chr4:88162600-88162800	Enhancers	HepG2	liver

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