Variant report

Variant	rs10090646
Chromosome Location	chr8:121840359-121840360
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	chr8:121839539..121841750-chr8:121853212..121856019,2	MCF-7	breast:
2	chr8:121831609..121834330-chr8:121840009..121841536,2	MCF-7	breast:

Extended variants
information (count: 8 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10091004	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10094866	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10109307	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10109356	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28625879	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35903599	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6469958	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.90[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	nsv1016172	chr8:121679590-121929916	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10090646	MED30	cis	cerebellum	SCAN
rs10090646	KLHL38	cis	parietal	SCAN
rs10090646	RNF139	cis	parietal	SCAN
rs10090646	LOC100131726	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:121835800-121840400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr8:121835800-121840400	Enhancers	NHDF-Ad	bronchial
3	chr8:121836200-121840600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr8:121837400-121840400	Enhancers	NHLF	lung
5	chr8:121837600-121843800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr8:121838200-121840600	Enhancers	Fetal Intestine Small	intestine
7	chr8:121838200-121841200	Enhancers	Fetal Intestine Large	intestine
8	chr8:121838400-121869800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr8:121839000-121840600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr8:121839200-121840400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr8:121839400-121842000	Weak transcription	Psoas Muscle	Psoas
12	chr8:121839600-121840600	Enhancers	Hela-S3	cervix
13	chr8:121839600-121840800	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr8:121839800-121840600	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr8:121839800-121840600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr8:121839800-121840600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr8:121840000-121840400	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr8:121840000-121840400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr8:121840000-121840400	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr8:121840000-121840600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr8:121840000-121840600	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr8:121840000-121840600	Flanking Active TSS	Liver	Liver
23	chr8:121840000-121840600	Enhancers	Duodenum Mucosa	Duodenum
24	chr8:121840200-121840600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr8:121840200-121840600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr8:121840200-121840600	Enhancers	Spleen	Spleen
27	chr8:121840200-121840600	Flanking Active TSS	HepG2	liver
28	chr8:121840200-121840600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links