Variant report

Variant	rs7835298
Chromosome Location	chr8:124552303-124552304
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:124530995..124533872-chr8:124550796..124552419,2	MCF-7	breast:
2	chr8:124551934..124554097-chr8:124626463..124629241,3	MCF-7	breast:
3	chr8:124525228..124528986-chr8:124549190..124552536,4	MCF-7	breast:
4	chr8:124542682..124546202-chr8:124550886..124554262,4	MCF-7	breast:
5	chr8:124509786..124511440-chr8:124550699..124553342,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000253286	Chromatin interaction
ENSG00000156804	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12678620	0.88[ASN][1000 genomes]
rs16898553	0.92[CHD][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs2280919	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2280920	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2280921	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2294090	0.83[JPT][hapmap];0.83[MEX][hapmap]
rs4436105	0.82[CEU][hapmap];0.83[JPT][hapmap];0.84[MEX][hapmap]
rs57111244	0.87[ASN][1000 genomes]
rs58078057	0.88[ASN][1000 genomes]
rs60841063	0.88[ASN][1000 genomes]
rs62521290	0.88[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	nsv831450	chr8:124471741-124661359	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7835298	NSMCE2	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:124542800-124552400	Weak transcription	Hela-S3	cervix
2	chr8:124548200-124552600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr8:124548600-124554000	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr8:124548800-124554400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr8:124549800-124552400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr8:124549800-124552800	Enhancers	Fetal Brain Male	brain
7	chr8:124549800-124553200	Flanking Active TSS	HUVEC	blood vessel
8	chr8:124549800-124553800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr8:124550000-124554000	Active TSS	Thymus	Thymus
10	chr8:124550200-124552600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr8:124550200-124554600	Active TSS	Fetal Brain Female	brain
12	chr8:124550400-124553400	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
13	chr8:124550600-124554200	Active TSS	HSMMtube	muscle
14	chr8:124550800-124552400	Weak transcription	GM12878-XiMat	blood
15	chr8:124550800-124552600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr8:124550800-124554200	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr8:124550800-124554200	Active TSS	Aorta	Aorta
18	chr8:124550800-124554200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr8:124550800-124554400	Active TSS	Ovary	ovary
20	chr8:124550800-124554400	Active TSS	Psoas Muscle	Psoas
21	chr8:124551200-124554000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr8:124551200-124554000	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr8:124551200-124554200	Active TSS	Brain Anterior Caudate	brain
24	chr8:124551200-124554200	Active TSS	Brain Substantia Nigra	brain
25	chr8:124551400-124552600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
26	chr8:124551400-124552600	Active TSS	Brain Germinal Matrix	brain
27	chr8:124551400-124554000	Active TSS	NHDF-Ad	bronchial
28	chr8:124551400-124554200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr8:124551400-124554200	Active TSS	Right Ventricle	heart
30	chr8:124551600-124552800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr8:124551600-124553000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
32	chr8:124551600-124553200	Active TSS	Fetal Heart	heart
33	chr8:124551600-124554000	Active TSS	Brain Cingulate Gyrus	brain
34	chr8:124551600-124554000	Active TSS	Rectal Mucosa Donor 29	rectum
35	chr8:124551800-124552400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
36	chr8:124551800-124552400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr8:124551800-124552600	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
38	chr8:124551800-124553200	Flanking Active TSS	NH-A	brain
39	chr8:124552000-124552400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
40	chr8:124552000-124552400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr8:124552000-124552400	Flanking Active TSS	Brain Angular Gyrus	brain
42	chr8:124552000-124552400	Flanking Active TSS	Duodenum Mucosa	Duodenum
43	chr8:124552000-124552400	Bivalent Enhancer	Fetal Lung	lung
44	chr8:124552000-124552400	Flanking Active TSS	Right Atrium	heart
45	chr8:124552000-124552400	Flanking Active TSS	Sigmoid Colon	Sigmoid Colon
46	chr8:124552000-124552600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
47	chr8:124552000-124552600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
48	chr8:124552000-124552600	Flanking Active TSS	Brain Hippocampus Middle	brain
49	chr8:124552000-124552600	Flanking Active TSS	Placenta	Placenta
50	chr8:124552000-124552600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links