Variant report

Variant	rs6440092
Chromosome Location	chr3:142313987-142313988
allele	A/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	JUND	chr3:142313947-142315442	T-47D	breast:	n/a	chr3:142314619-142314630
2	ESR1	chr3:142313930-142314615	T-47D	breast:	n/a	n/a
3	GATA3	chr3:142313916-142315743	T-47D	breast:	n/a	chr3:142315041-142315058 chr3:142315364-142315373 chr3:142314319-142314329 chr3:142314320-142314327 chr3:142314321-142314338
4	FOXA1	chr3:142313885-142314329	T-47D	breast:	n/a	n/a
5	GATA3	chr3:142313739-142315644	MCF-7	breast:	n/a	chr3:142315041-142315058 chr3:142315364-142315373 chr3:142314319-142314329 chr3:142314320-142314327 chr3:142314321-142314338
6	EP300	chr3:142313881-142314354	T-47D	breast:	n/a	n/a
7	GATA3	chr3:142313910-142315602	MCF-7	breast:	n/a	chr3:142315041-142315058 chr3:142315364-142315373 chr3:142314319-142314329 chr3:142314320-142314327 chr3:142314321-142314338
8	GATA3	chr3:142313823-142315414	T-47D	breast:	n/a	chr3:142315041-142315058 chr3:142315364-142315373 chr3:142314319-142314329 chr3:142314320-142314327 chr3:142314321-142314338
9	GATA3	chr3:142313799-142314333	SH-SY5Y	brain:	n/a	chr3:142314319-142314329 chr3:142314320-142314327
10	JUND	chr3:142313881-142315494	T-47D	breast:	n/a	chr3:142314619-142314630

No.	Distal block	Cell Line	Cell type
1	chr3:142297466..142299799-chr3:142313558..142315620,3	K562	blood:
2	chr3:142313766..142316499-chr3:142498136..142500635,2	K562	blood:
3	chr3:142294568..142300006-chr3:142310942..142319455,13	MCF-7	breast:
4	chr3:142313378..142316741-chr3:142442748..142446550,8	K562	blood:
5	chr3:142294183..142301262-chr3:142311308..142318922,13	MCF-7	breast:
6	chr3:142312229..142317018-chr3:142442889..142445391,9	K562	blood:
7	chr3:142296149..142300233-chr3:142313670..142315817,6	K562	blood:
8	chr3:142312435..142314889-chr3:142442565..142445180,3	MCF-7	breast:
9	chr3:142313218..142314887-chr3:142348977..142351077,2	K562	blood:

Variant related genes	Relation type
PLS1	TF binding region
RNA5SP143	TF binding region
ENSG00000242390	Chromatin interaction
ENSG00000144935	Chromatin interaction
ENSG00000175054	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10935465	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1129393	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13065075	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13067795	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13069307	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13085998	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13093869	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13098343	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1357529	0.88[EUR][1000 genomes]
rs1357530	0.90[EUR][1000 genomes]
rs1916639	0.90[EUR][1000 genomes]
rs1983434	0.90[EUR][1000 genomes]
rs1983435	0.90[EUR][1000 genomes]
rs2030613	0.91[EUR][1000 genomes]
rs2049325	0.91[EUR][1000 genomes]
rs2049326	0.91[EUR][1000 genomes]
rs2140432	0.91[EUR][1000 genomes]
rs2177396	0.91[EUR][1000 genomes]
rs2227928	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2227930	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2354860	0.89[EUR][1000 genomes]
rs28617475	0.80[ASN][1000 genomes]
rs3922730	0.82[EUR][1000 genomes]
rs4273389	0.84[EUR][1000 genomes]
rs4413348	0.91[EUR][1000 genomes]
rs4597728	0.83[EUR][1000 genomes]
rs6414350	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440086	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6440087	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6440088	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6440089	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6440090	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6440091	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440093	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440094	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440098	0.89[EUR][1000 genomes]
rs6440099	0.90[EUR][1000 genomes]
rs6768093	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6770155	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775583	0.83[EUR][1000 genomes]
rs6775718	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6775813	0.90[EUR][1000 genomes]
rs6780250	0.83[EUR][1000 genomes]
rs6782400	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6783203	0.90[EUR][1000 genomes]
rs6784089	0.90[EUR][1000 genomes]
rs6785675	0.82[EUR][1000 genomes]
rs6791816	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6792259	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6799752	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6802734	0.86[EUR][1000 genomes]
rs6802774	0.86[EUR][1000 genomes]
rs7428496	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7609842	0.84[EUR][1000 genomes]
rs7610557	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615316	0.90[EUR][1000 genomes]
rs7623524	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7630130	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7631313	0.89[EUR][1000 genomes]
rs7634158	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7635146	0.90[EUR][1000 genomes]
rs7641330	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7646880	0.91[EUR][1000 genomes]
rs7647573	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7651071	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7651542	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9683085	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9808914	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9808943	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9816736	0.82[EUR][1000 genomes]
rs9820353	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9820770	0.82[EUR][1000 genomes]
rs9824176	0.85[EUR][1000 genomes]
rs9824893	0.91[EUR][1000 genomes]
rs9825207	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9828178	0.82[EUR][1000 genomes]
rs9846960	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9855140	0.84[EUR][1000 genomes]
rs9855919	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9866958	0.90[EUR][1000 genomes]
rs9869842	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9876254	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9879995	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9882763	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877556	chr3:141898980-142331360	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv877558	chr3:142123841-142331360	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv877559	chr3:142132749-142331360	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv877560	chr3:142132749-142362179	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv877561	chr3:142152925-142331360	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
6	nsv932989	chr3:142204208-142423305	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142298200-142314400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:142298600-142314400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:142306200-142314400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr3:142306200-142314400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:142306200-142314400	Weak transcription	HSMMtube	muscle
6	chr3:142311200-142314400	Weak transcription	NHLF	lung
7	chr3:142313400-142314200	Enhancers	Pancreatic Islets	Pancreatic Islet
8	chr3:142313600-142314200	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr3:142313600-142314200	Enhancers	Stomach Mucosa	stomach
10	chr3:142313800-142314000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr3:142313800-142314200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr3:142313800-142314200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:142313800-142314200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:142313800-142314200	Enhancers	A549	lung
15	chr3:142313800-142314400	Enhancers	Fetal Kidney	kidney

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