Variant report

Variant	rs2930328
Chromosome Location	chr7:140358461-140358462
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:140358422..140360016-chr7:140372833..140375314,2	MCF-7	breast:
2	chr7:140357221..140358840-chr7:140396277..140397974,2	MCF-7	breast:
3	chr7:140358444..140360553-chr7:140370671..140372780,2	MCF-7	breast:
4	chr7:140356234..140358588-chr7:140371842..140375478,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000090266	Chromatin interaction
ENSG00000146966	Chromatin interaction
ENSG00000240889	Chromatin interaction
ENSG00000133597	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1106846	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1140034	0.89[MKK][hapmap]
rs2364397	0.88[MKK][hapmap]
rs2364399	0.81[MKK][hapmap]
rs28828674	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28896544	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2908235	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2930315	0.82[CEU][hapmap]
rs2930320	1.00[CEU][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap]
rs2930325	0.85[CEU][hapmap];1.00[CHD][hapmap]
rs2930326	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2930329	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2930330	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2930332	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2968546	0.85[CEU][hapmap]
rs2968550	0.89[MKK][hapmap]
rs2968553	0.89[MKK][hapmap]
rs2968559	0.89[MKK][hapmap]
rs2968560	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6464937	0.89[MKK][hapmap]
rs6969644	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6977496	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7785630	0.82[CEU][hapmap];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7802537	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7803697	0.89[MKK][hapmap]

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	nsv831157	chr7:140241339-140426876	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2930328	TRIM24	cis	parietal	SCAN
rs2930328	ZYX	cis	cerebellum	SCAN
rs2930328	ADCK2	cis	multi-tissue	Pritchard
rs2930328	ADCK2	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140357000-140361000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr7:140357200-140360200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr7:140357400-140358800	Weak transcription	Duodenum Mucosa	Duodenum
4	chr7:140357400-140358800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr7:140357400-140359200	Weak transcription	GM12878-XiMat	blood
6	chr7:140357400-140361200	Weak transcription	Placenta	Placenta
7	chr7:140357400-140361200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr7:140357600-140359600	Weak transcription	Fetal Muscle Leg	muscle
9	chr7:140358200-140359600	Weak transcription	Fetal Muscle Trunk	muscle
10	chr7:140358200-140359800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr7:140358400-140358600	Enhancers	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links