Variant report

Variant	rs6879127
Chromosome Location	chr5:36244666-36244667
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	GATA3	chr5:36244436-36244762	T-47D	breast:	n/a	chr5:36244565-36244575 chr5:36244564-36244580 chr5:36244568-36244575
2	GATA2	chr5:36244411-36244899	SH-SY5Y	brain:	n/a	chr5:36244565-36244575 chr5:36244564-36244580 chr5:36244568-36244575
3	GATA3	chr5:36244131-36244851	T-47D	breast:	n/a	chr5:36244565-36244575 chr5:36244564-36244580 chr5:36244568-36244575
4	GATA3	chr5:36244479-36244784	SH-SY5Y	brain:	n/a	chr5:36244565-36244575 chr5:36244564-36244580 chr5:36244568-36244575

No.	Distal block	Cell Line	Cell type
1	chr5:36244423..36246037-chr5:36247786..36250597,2	MCF-7	breast:
2	chr5:36150463..36155255-chr5:36239958..36244873,10	K562	blood:
3	chr5:36150467..36154483-chr5:36238242..36244873,13	K562	blood:

Variant related genes	Relation type
NADK2	TF binding region
ENSG00000164187	Chromatin interaction
ENSG00000145604	Chromatin interaction
ENSG00000201223	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10512639	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10941278	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10941279	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10941281	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11737918	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11738615	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11739323	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11744207	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11745827	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11747546	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12522905	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13180677	0.81[EUR][1000 genomes]
rs1363840	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16902835	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2362977	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2362979	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28610396	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35161198	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35647151	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3761973	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3789758	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3933496	0.81[ASN][1000 genomes]
rs67061065	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67399512	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6881318	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6884331	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6890702	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72744549	0.85[ASN][1000 genomes]
rs72744564	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72744565	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72744587	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72744593	0.80[ASN][1000 genomes]
rs732328	0.80[EUR][1000 genomes]
rs7716788	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830262	chr5:36074311-36293872	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	63 gene(s)	inside rSNPs	diseases
2	nsv1015638	chr5:36203646-36312576	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:36243000-36245800	Weak transcription	Ovary	ovary
2	chr5:36243200-36245800	Weak transcription	Placenta	Placenta
3	chr5:36243200-36246600	Weak transcription	Fetal Stomach	stomach
4	chr5:36243200-36247000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr5:36243200-36248000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr5:36243200-36252600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr5:36243400-36246800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr5:36243400-36252800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr5:36243400-36253200	Weak transcription	Aorta	Aorta
10	chr5:36243800-36245000	Enhancers	Liver	Liver
11	chr5:36244400-36244800	Enhancers	Primary T cells from cord blood	blood
12	chr5:36244600-36244800	Enhancers	Brain Cingulate Gyrus	brain

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