Variant report

Variant	rs7923541
Chromosome Location	chr10:99279160-99279161
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:99275579..99277366-chr10:99277998..99279617,2	MCF-7	breast:
2	chr10:99278192..99281004-chr10:99284168..99285856,2	MCF-7	breast:
3	chr10:99272672..99275442-chr10:99278797..99280521,2	K562	blood:
4	chr10:99275110..99276891-chr10:99277737..99279541,2	MCF-7	breast:
5	chr10:99275538..99279686-chr10:99333593..99336127,3	MCF-7	breast:
6	chr10:99257631..99259824-chr10:99278318..99280572,2	K562	blood:

Variant related genes	Relation type
ENSG00000165886	Chromatin interaction
ENSG00000155229	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10882938	0.81[CHB][hapmap]
rs10882942	0.81[CHB][hapmap]
rs11189245	0.86[CHB][hapmap]
rs11189274	0.81[CHB][hapmap]
rs11814566	0.81[CHB][hapmap]
rs1417408	0.81[CHB][hapmap]
rs2236575	0.81[CHB][hapmap]
rs3740526	0.81[CHB][hapmap]
rs4917774	0.91[CHB][hapmap];0.88[CHD][hapmap]
rs4919105	0.95[CHB][hapmap];0.93[CHD][hapmap]
rs7068965	0.81[CHB][hapmap]
rs7075656	0.95[CHB][hapmap]
rs7096611	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1817777	chr10:99196035-99558169	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv1036494	chr10:99267639-99345207	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7923541	WNT8B	cis	cerebellum	SCAN
rs7923541	COX15	cis	cerebellum	SCAN
rs7923541	CC2D2B	cis	cerebellum	SCAN
rs7923541	FRAT2	cis	cerebellum	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99270800-99286200	Enhancers	Skeletal Muscle Female	skeletal muscle
2	chr10:99271200-99279200	Enhancers	Skeletal Muscle Male	skeletal muscle
3	chr10:99273800-99283200	Enhancers	Fetal Muscle Leg	muscle
4	chr10:99273800-99283200	Enhancers	Left Ventricle	heart
5	chr10:99274200-99279600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr10:99274200-99285000	Enhancers	Right Ventricle	heart
7	chr10:99274400-99280200	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr10:99274600-99279800	Enhancers	Brain Substantia Nigra	brain
9	chr10:99274800-99279400	Enhancers	Adipose Nuclei	Adipose
10	chr10:99275000-99293800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr10:99276000-99284400	Weak transcription	HepG2	liver
12	chr10:99276600-99279400	Enhancers	HMEC	breast
13	chr10:99276600-99279800	Enhancers	HUVEC	blood vessel
14	chr10:99276800-99279600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr10:99276800-99279800	Enhancers	Brain Hippocampus Middle	brain
16	chr10:99276800-99280000	Enhancers	HSMM	muscle
17	chr10:99276800-99281400	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr10:99277000-99279400	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr10:99277000-99279600	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr10:99277000-99279800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr10:99277000-99280400	Enhancers	Fetal Lung	lung
22	chr10:99277200-99279400	Enhancers	Brain Cingulate Gyrus	brain
23	chr10:99277200-99279800	Enhancers	Muscle Satellite Cultured Cells	--
24	chr10:99277200-99282800	Enhancers	HSMMtube	muscle
25	chr10:99277400-99279200	Enhancers	Psoas Muscle	Psoas
26	chr10:99277400-99279400	Enhancers	Brain Anterior Caudate	brain
27	chr10:99277400-99279400	Enhancers	NH-A	brain
28	chr10:99277400-99279800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr10:99277400-99279800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr10:99277400-99279800	Enhancers	Brain Angular Gyrus	brain
31	chr10:99277400-99280000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr10:99277600-99279600	Enhancers	NHDF-Ad	bronchial
33	chr10:99277600-99279800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr10:99277800-99279400	Enhancers	NHLF	lung
35	chr10:99277800-99279600	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr10:99277800-99279600	Enhancers	Osteobl	bone
37	chr10:99277800-99279800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr10:99277800-99281800	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr10:99277800-99301800	Weak transcription	Gastric	stomach
40	chr10:99278000-99279800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr10:99278000-99279800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr10:99278000-99302600	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr10:99278200-99279200	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr10:99278200-99280400	Weak transcription	Pancreas	Pancrea
45	chr10:99278200-99281600	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr10:99278200-99298800	Weak transcription	Aorta	Aorta
47	chr10:99278400-99279200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr10:99278400-99280000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr10:99278400-99280200	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr10:99278400-99281800	Weak transcription	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links