Variant report

Variant	rs10804689
Chromosome Location	chr3:143057379-143057380
allele	A/G
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	SRF	chr3:143056967-143057458	ECC-1	luminal epithelium:	n/a	chr3:143057178-143057191 chr3:143057178-143057189 chr3:143057180-143057191 chr3:143057180-143057189 chr3:143057176-143057193 chr3:143057175-143057193 chr3:143057179-143057190 chr3:143057177-143057192 chr3:143057176-143057190 chr3:143057175-143057189 chr3:143057179-143057193
2	RAD21	chr3:143057180-143057660	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:143055149..143058729-chr3:143058882..143061743,3	K562	blood:
2	chr3:143049101..143052451-chr3:143056626..143059965,3	K562	blood:

Variant related genes	Relation type
SLC9A9-AS1	TF binding region
ENSG00000240012	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10446325	0.92[CHB][hapmap];0.95[JPT][hapmap]
rs10804690	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10804691	0.92[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs10935488	0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10935489	0.92[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs11915857	0.83[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs12493355	0.92[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs12633063	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs13066661	0.84[CHB][hapmap];0.85[JPT][hapmap]
rs13067348	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs1393071	0.92[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1501628	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1501629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1550547	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs16853428	0.83[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs16853431	0.91[ASN][1000 genomes]
rs1837784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2165518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2352725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2883015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6440163	0.92[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs6440164	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6768217	0.84[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs6769555	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6770495	0.80[CHB][hapmap]
rs6806677	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs729509	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs729511	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7632299	0.92[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs7652901	0.82[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs9332458	0.92[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs963885	0.83[CHB][hapmap]
rs968586	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs968587	0.96[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	esv2757894	chr3:142992697-143285979	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv2759184	chr3:142992697-143285979	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143049200-143061200	Weak transcription	Fetal Thymus	thymus
2	chr3:143052600-143061600	Weak transcription	Dnd41	blood
3	chr3:143056200-143057400	Enhancers	Fetal Kidney	kidney
4	chr3:143056400-143057400	Enhancers	Aorta	Aorta
5	chr3:143056800-143058000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:143056800-143058000	Weak transcription	Placenta	Placenta
7	chr3:143056800-143058800	Enhancers	Fetal Lung	lung
8	chr3:143056800-143062400	Weak transcription	Primary T cells from cord blood	blood
9	chr3:143057000-143057400	Enhancers	Fetal Heart	heart

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