Variant report

Variant	rs6879339
Chromosome Location	chr5:5306128-5306129
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:5302322..5304229-chr5:5305054..5307757,2	K562	blood:
2	chr5:5304478..5306308-chr5:5307574..5310216,2	MCF-7	breast:
3	chr5:5304202..5306167-chr5:5310492..5313032,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10069877	0.89[AMR][1000 genomes]
rs10071930	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10512779	0.93[AMR][1000 genomes]
rs11134107	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11134108	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11134109	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11749585	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12109856	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12109945	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12110152	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12163941	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12513662	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12518997	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12521040	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12521610	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13155606	0.97[ASN][1000 genomes]
rs13170260	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13172105	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13187616	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13188613	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16875268	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4473739	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4478285	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4535428	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4702254	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57953413	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6555346	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6555347	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6555348	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6555350	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6555351	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6555352	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6555353	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67272384	0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7706744	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7706767	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7720820	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[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	nsv1024784	chr5:4980979-5391231	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1032719	chr5:5102763-5387406	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537621	chr5:5102763-5387406	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv1793859	chr5:5298350-5309672	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
5	esv3352829	chr5:5304052-5306650	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:5302400-5312400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr5:5302600-5307400	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr5:5302800-5307000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr5:5304000-5307800	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr5:5304800-5306600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr5:5304800-5312200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr5:5305000-5306800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:5305000-5311400	Strong transcription	Ovary	ovary
9	chr5:5305200-5306800	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr5:5305400-5306400	Weak transcription	HMEC	breast
11	chr5:5305400-5306800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr5:5305400-5307000	Weak transcription	NHEK	skin
13	chr5:5305600-5306600	Weak transcription	NH-A	brain
14	chr5:5305600-5307000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr5:5305600-5307600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr5:5305600-5308200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr5:5305600-5308200	Enhancers	Fetal Lung	lung
18	chr5:5305600-5309800	Weak transcription	Right Atrium	heart
19	chr5:5305600-5312000	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr5:5305600-5312800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr5:5305600-5312800	Weak transcription	Psoas Muscle	Psoas
22	chr5:5305600-5314800	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr5:5305600-5319400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr5:5305600-5326200	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr5:5305800-5307600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr5:5305800-5307800	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr5:5305800-5309800	Weak transcription	Pancreas	Pancrea
28	chr5:5305800-5321400	Weak transcription	Fetal Kidney	kidney
29	chr5:5306000-5308000	Enhancers	Fetal Muscle Leg	muscle
30	chr5:5306000-5309800	Weak transcription	Esophagus	oesophagus

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