Variant report

Variant	rs6899752
Chromosome Location	chr6:53610819-53610820
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:53610265..53615014-chr6:53656858..53662694,9	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KLHL31-2	chr6:53610490-53611401	XLOC_005748

Variant related genes	Relation type
ENSG00000228614	Chromatin interaction
ENSG00000137269	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10948779	0.89[EUR][1000 genomes]
rs11755346	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13220665	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3000996	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3000997	0.89[EUR][1000 genomes]
rs3000999	0.88[EUR][1000 genomes]
rs3001000	0.88[EUR][1000 genomes]
rs3001001	0.88[EUR][1000 genomes]
rs3001002	0.86[EUR][1000 genomes]
rs3001009	0.85[EUR][1000 genomes]
rs3001010	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3003489	0.85[EUR][1000 genomes]
rs3003491	0.85[EUR][1000 genomes]
rs3003493	0.85[EUR][1000 genomes]
rs3003500	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3003501	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34165049	0.94[EUR][1000 genomes]
rs34861916	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34880762	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35389351	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35517171	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35756855	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813849	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4236113	0.85[EUR][1000 genomes]
rs4265033	0.86[EUR][1000 genomes]
rs4276502	0.88[EUR][1000 genomes]
rs4286781	0.85[EUR][1000 genomes]
rs4321822	0.95[EUR][1000 genomes]
rs4326237	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4336450	0.89[EUR][1000 genomes]
rs4351263	0.83[EUR][1000 genomes]
rs4382260	0.85[EUR][1000 genomes]
rs4398733	0.85[EUR][1000 genomes]
rs4437471	0.84[EUR][1000 genomes]
rs4484515	0.85[EUR][1000 genomes]
rs4489155	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4591854	0.85[EUR][1000 genomes]
rs4615391	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4712048	0.85[EUR][1000 genomes]
rs4712049	0.85[EUR][1000 genomes]
rs4715424	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715426	0.85[EUR][1000 genomes]
rs59641455	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60035355	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458957	0.89[EUR][1000 genomes]
rs6458958	0.86[EUR][1000 genomes]
rs6458959	0.86[EUR][1000 genomes]
rs6458961	0.84[EUR][1000 genomes]
rs6458962	0.84[EUR][1000 genomes]
rs6458965	0.85[EUR][1000 genomes]
rs6458966	0.85[EUR][1000 genomes]
rs6458969	0.85[EUR][1000 genomes]
rs6650996	0.84[EUR][1000 genomes]
rs6920743	0.86[EUR][1000 genomes]
rs6924025	0.85[EUR][1000 genomes]
rs6925836	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6926478	0.85[EUR][1000 genomes]
rs6937901	0.85[EUR][1000 genomes]
rs71555560	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7739965	0.85[EUR][1000 genomes]
rs7753504	0.85[EUR][1000 genomes]
rs7754791	0.85[EUR][1000 genomes]
rs7759946	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7762883	0.84[EUR][1000 genomes]
rs7763081	0.85[EUR][1000 genomes]
rs7763147	0.86[EUR][1000 genomes]
rs7769893	0.89[EUR][1000 genomes]
rs9296719	0.85[EUR][1000 genomes]
rs9296721	0.83[EUR][1000 genomes]
rs9367544	0.82[EUR][1000 genomes]
rs9370235	0.85[EUR][1000 genomes]
rs9370239	0.83[EUR][1000 genomes]
rs9382234	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9382237	0.89[EUR][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	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1021506	chr6:53600338-53770482	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 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	chr6:53601600-53638000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr6:53601800-53613400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr6:53602200-53614800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr6:53606400-53611200	Weak transcription	HepG2	liver
5	chr6:53606400-53619600	Weak transcription	Right Atrium	heart
6	chr6:53606600-53611400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr6:53609000-53612200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:53609800-53611000	Enhancers	Esophagus	oesophagus
9	chr6:53610200-53611600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr6:53610200-53611600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:53610200-53614000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr6:53610600-53611200	Enhancers	NHEK	skin
13	chr6:53610600-53612200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr6:53610600-53612200	Enhancers	HMEC	breast
15	chr6:53610800-53611600	Weak transcription	Placenta	Placenta

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