Variant report

Variant	rs28366687
Chromosome Location	chr6:28059766-28059767
allele	C/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	MXI1	chr6:28058448-28059996	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
ZSCAN12P1	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10946952	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1150669	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1150671	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11965542	0.91[EUR][1000 genomes]
rs11966237	0.91[EUR][1000 genomes]
rs11966528	1.00[AMR][1000 genomes]
rs11967622	1.00[EUR][1000 genomes]
rs11969150	0.91[EUR][1000 genomes]
rs12333002	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1233667	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1233698	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1233702	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61072813	1.00[AMR][1000 genomes]
rs62638680	0.91[EUR][1000 genomes]
rs6908414	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6910942	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6922530	1.00[AMR][1000 genomes]
rs6924324	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6928131	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6932313	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6932394	0.91[EUR][1000 genomes]
rs73385806	0.91[EUR][1000 genomes]
rs73385807	0.91[EUR][1000 genomes]
rs73385810	0.91[EUR][1000 genomes]
rs73385818	0.91[EUR][1000 genomes]
rs73385870	0.91[EUR][1000 genomes]
rs73386660	1.00[AMR][1000 genomes]
rs73392701	1.00[AMR][1000 genomes]
rs73398516	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73400525	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73400579	1.00[EUR][1000 genomes]
rs73400580	0.91[EUR][1000 genomes]
rs73400590	0.91[EUR][1000 genomes]
rs73402513	0.91[EUR][1000 genomes]
rs7748537	1.00[AMR][1000 genomes]
rs9461421	1.00[AMR][1000 genomes]
rs9461422	0.89[AMR][1000 genomes]
rs9468253	1.00[AMR][1000 genomes]
rs9468257	1.00[AMR][1000 genomes]
rs9468261	1.00[AMR][1000 genomes]
rs9468262	1.00[AMR][1000 genomes]
rs9468269	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468291	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468293	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468305	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9468306	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830619	chr6:27872302-28062544	Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription 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	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28049600-28063000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr6:28050800-28061200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr6:28053400-28064600	Strong transcription	Placenta	Placenta
4	chr6:28055400-28059800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr6:28057800-28060400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr6:28057800-28065800	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr6:28058000-28060200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr6:28058000-28060400	Weak transcription	NHEK	skin
9	chr6:28058000-28060600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:28058000-28064800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr6:28058200-28062200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr6:28058200-28062200	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr6:28058200-28072200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:28058400-28060800	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr6:28058400-28061200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr6:28058800-28072000	Weak transcription	HMEC	breast
17	chr6:28059200-28059800	Active TSS	Fetal Brain Male	brain
18	chr6:28059200-28061000	Weak transcription	Lung	lung
19	chr6:28059200-28061200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr6:28059200-28063000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr6:28059200-28063200	Weak transcription	Pancreas	Pancrea
22	chr6:28059200-28063400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr6:28059200-28066800	Weak transcription	Esophagus	oesophagus
24	chr6:28059400-28059800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr6:28059400-28059800	Enhancers	Fetal Heart	heart
26	chr6:28059400-28059800	Enhancers	Fetal Kidney	kidney
27	chr6:28059400-28060400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr6:28059400-28061600	Weak transcription	Ovary	ovary
29	chr6:28059400-28062000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr6:28059400-28062000	Weak transcription	Fetal Stomach	stomach
31	chr6:28059400-28062600	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr6:28059400-28072000	Weak transcription	Brain Substantia Nigra	brain

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