Variant report

Variant	rs956796
Chromosome Location	chr1:150186091-150186092
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:150182720..150184289-chr1:150184985..150187517,2	MCF-7	breast:
2	chr1:150185872..150186601-chr1:150402045..150402899,3	MCF-7	breast:
3	chr1:149956254..149958159-chr1:150184298..150186686,2	MCF-7	breast:
4	chr1:150185925..150186466-chr1:150253711..150254243,2	MCF-7	breast:
5	chr1:150184759..150186606-chr1:150253891..150255792,2	MCF-7	breast:
6	chr1:149854142..149859760-chr1:150182757..150186625,7	MCF-7	breast:
7	chr1:150185544..150187613-chr1:150191565..150193238,2	MCF-7	breast:
8	chr1:150185905..150189202-chr1:150204960..150208928,4	MCF-7	breast:
9	chr1:150184319..150187106-chr1:150241598..150243125,2	MCF-7	breast:
10	chr1:150184020..150189547-chr1:150205905..150210191,12	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000184678	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000266187	Chromatin interaction
ENSG00000143401	Chromatin interaction
ENSG00000222222	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000117362	Chromatin interaction
ENSG00000159208	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs12027008	1.00[ASW][hapmap]
rs2275780	1.00[ASW][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	nsv529719	chr1:150006344-150311095	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs956796	TMOD4	cis	cerebellum	SCAN
rs956796	CTSS	cis	cerebellum	SCAN
rs956796	MRPS21	cis	cerebellum	SCAN
rs956796	MRPS21	cis	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150184200-150195800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:150184200-150206600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:150185400-150186200	Enhancers	Stomach Mucosa	stomach
4	chr1:150185400-150186200	Enhancers	Spleen	Spleen
5	chr1:150185400-150186600	Active TSS	Brain Anterior Caudate	brain
6	chr1:150185400-150186800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
7	chr1:150185400-150186800	Flanking Active TSS	Dnd41	blood
8	chr1:150185600-150186200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:150185600-150186200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
10	chr1:150185600-150186200	Active TSS	Cortex derived primary cultured neurospheres	brain
11	chr1:150185600-150186200	Flanking Active TSS	HepG2	liver
12	chr1:150185600-150186200	Flanking Active TSS	NHEK	skin
13	chr1:150185600-150186400	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr1:150185600-150186400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:150185600-150186400	Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr1:150185600-150186400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:150185600-150186400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:150185600-150186400	Active TSS	Primary T cells from cord blood	blood
19	chr1:150185600-150186400	Active TSS	Brain Angular Gyrus	brain
20	chr1:150185600-150186400	Active TSS	Colonic Mucosa	Colon
21	chr1:150185600-150186400	Active TSS	Fetal Brain Female	brain
22	chr1:150185600-150186400	Active TSS	Rectal Mucosa Donor 31	rectum
23	chr1:150185600-150186400	Active TSS	Thymus	Thymus
24	chr1:150185600-150186400	Active TSS	NHLF	lung
25	chr1:150185600-150186600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:150185600-150186600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr1:150185600-150186600	Active TSS	Psoas Muscle	Psoas
28	chr1:150185600-150186600	Active TSS	Rectal Mucosa Donor 29	rectum
29	chr1:150185600-150186600	Active TSS	Right Atrium	heart
30	chr1:150185600-150186800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr1:150185600-150186800	Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr1:150185600-150186800	Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr1:150185600-150186800	Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr1:150185600-150186800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:150185600-150186800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
36	chr1:150185600-150186800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
37	chr1:150185600-150186800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr1:150185600-150186800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr1:150185600-150186800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr1:150185600-150186800	Active TSS	Fetal Kidney	kidney
41	chr1:150185600-150186800	Active TSS	Fetal Lung	lung
42	chr1:150185600-150186800	Active TSS	Rectal Smooth Muscle	rectum
43	chr1:150185600-150186800	Flanking Active TSS	Osteobl	bone
44	chr1:150185800-150186200	Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr1:150185800-150186200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr1:150185800-150186200	Active TSS	Brain Germinal Matrix	brain
47	chr1:150185800-150186200	Active TSS	Monocytes-CD14+_RO01746	blood
48	chr1:150185800-150186400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
49	chr1:150185800-150186400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr1:150185800-150186400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links