Variant report

Variant	rs5997400
Chromosome Location	chr22:29167222-29167223
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr22:29167183-29167389	HepG2	liver:	n/a	n/a
2	GATA3	chr22:29167170-29167492	T-47D	breast:	n/a	n/a
3	FOXA1	chr22:29167134-29167480	T-47D	breast:	n/a	n/a
4	FOXA1	chr22:29167119-29167457	T-47D	breast:	n/a	n/a
5	GATA3	chr22:29167075-29167555	T-47D	breast:	n/a	n/a
6	FOXA1	chr22:29167209-29167494	HepG2	liver:	n/a	n/a
7	EP300	chr22:29167174-29167469	T-47D	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:29165808..29174203-chr22:29186827..29200037,34	MCF-7	breast:
2	chr22:29162785..29164822-chr22:29166459..29168547,3	MCF-7	breast:
3	chr22:29166664..29171376-chr22:29189061..29194611,6	MCF-7	breast:
4	chr22:29134226..29139597-chr22:29164663..29170736,9	K562	blood:
5	chr22:29167147..29172880-chr22:29212986..29217151,7	MCF-7	breast:
6	chr22:29134212..29140528-chr22:29167074..29172462,20	MCF-7	breast:

No data

Variant related genes	Relation type
CCDC117	TF binding region
ENSG00000183765	Chromatin interaction
ENSG00000100219	Chromatin interaction
ENSG00000100209	Chromatin interaction
ENSG00000226471	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs12159764	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs132530	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs16986714	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1894590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2269575	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41281601	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4484131	0.82[ASN][1000 genomes]
rs5762799	0.81[YRI][hapmap]
rs57652775	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59954406	0.86[ASN][1000 genomes]
rs5997399	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5997403	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5997404	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6005875	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6005876	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6005878	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6005879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6005893	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6005900	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6005905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6005906	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6005907	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6005915	0.83[ASW][hapmap];0.88[YRI][hapmap]
rs6005918	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6005920	0.86[ASN][1000 genomes]
rs60513698	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6519764	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7284322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7290019	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7290679	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7290958	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7291783	0.81[ASN][1000 genomes]
rs73388819	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73388827	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73388828	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73388838	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73388841	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73399615	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73399621	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9941965	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	nsv916473	chr22:28837041-29215603	Weak transcription Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv9895	chr22:29029961-29184277	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers 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 target site	92 gene(s)	inside rSNPs	diseases
4	nsv834169	chr22:29095446-29303929	Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29145800-29168000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr22:29154400-29167400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr22:29165800-29168600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr22:29167000-29168600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr22:29167200-29167600	Flanking Active TSS	HepG2	liver
6	chr22:29167200-29168200	Enhancers	HMEC	breast
7	chr22:29167200-29168200	Enhancers	NHEK	skin
8	chr22:29167200-29168400	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr22:29167200-29168400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr22:29167200-29168400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr22:29167200-29168400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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