Variant report

Variant	rs2582778
Chromosome Location	chr8:49838908-49838909
allele	A/C
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	chr8:49837854-49839237	SK-N-SH	brain:	n/a	chr8:49838573-49838582
2	RAD21	chr8:49837442-49839138	SK-N-SH	brain:	n/a	chr8:49838357-49838366 chr8:49838348-49838367
3	ATF1	chr8:49838233-49838998	K562	blood:	n/a	n/a
4	JUND	chr8:49838039-49838944	Hela-S3	cervix:	n/a	chr8:49838573-49838582
5	CTCF	chr8:49837517-49839064	A549	lung:	n/a	chr8:49838357-49838364 chr8:49838351-49838367 chr8:49838350-49838368 chr8:49838352-49838365 chr8:49838345-49838366
6	CTCF	chr8:49837681-49839012	HCT-116	colon:	n/a	chr8:49838357-49838364 chr8:49838351-49838367 chr8:49838350-49838368 chr8:49838352-49838365 chr8:49838345-49838366
7	CTCF	chr8:49837455-49838982	SK-N-SH	brain:	n/a	chr8:49838357-49838364 chr8:49838351-49838367 chr8:49838350-49838368 chr8:49838352-49838365 chr8:49838345-49838366
8	SMC3	chr8:49837533-49839089	SK-N-SH	brain:	n/a	chr8:49838352-49838366

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:49426786..49427372-chr8:49837914..49838955,3	MCF-7	breast:
2	chr8:49837099..49839896-chr8:49842697..49845711,3	K562	blood:

Variant related genes	Relation type
SNAI2	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10097264	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10100077	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10808734	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11515036	0.81[EUR][1000 genomes]
rs1441004	0.84[EUR][1000 genomes]
rs1441005	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1992375	0.85[CEU][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs2385117	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][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	nsv890854	chr8:49738821-49838908	Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2582778	SNTG1	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:49835000-49840200	Enhancers	Placenta Amnion	Placenta Amnion
2	chr8:49835800-49839000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr8:49836200-49839200	Enhancers	Fetal Lung	lung
4	chr8:49836800-49839000	Enhancers	Dnd41	blood
5	chr8:49836800-49843200	Weak transcription	Esophagus	oesophagus
6	chr8:49837800-49839000	Enhancers	NH-A	brain
7	chr8:49837800-49839200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr8:49837800-49846200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr8:49838000-49839000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr8:49838000-49839000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr8:49838000-49840000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr8:49838000-49841600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr8:49838000-49841600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr8:49838200-49839000	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr8:49838200-49839000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr8:49838200-49839000	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr8:49838600-49839000	Enhancers	Primary T cells from cord blood	blood
18	chr8:49838600-49843000	Weak transcription	Osteobl	bone
19	chr8:49838800-49839000	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr8:49838800-49839000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr8:49838800-49840000	Weak transcription	Thymus	Thymus
22	chr8:49838800-49841400	Weak transcription	HMEC	breast
23	chr8:49838800-49841600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr8:49838800-49841800	Weak transcription	NHEK	skin
25	chr8:49838800-49842000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr8:49838800-49843000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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