Variant report

Variant	rs1408101
Chromosome Location	chr9:85834349-85834350
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:85818705..85819261-chr9:85834295..85835039,2	MCF-7	breast:
2	chr9:85834296..85835171-chr9:85845740..85846677,8	MCF-7	breast:
3	chr9:85576162..85576940-chr9:85834338..85835195,3	MCF-7	breast:
4	chr9:85813794..85816602-chr9:85833659..85835490,2	MCF-7	breast:
5	chr9:85834318..85834922-chr9:85942136..85942786,2	MCF-7	breast:
6	chr9:85832727..85836639-chr9:86319596..86323973,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251776	Chromatin interaction
ENSG00000254473	Chromatin interaction
ENSG00000135018	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10125314	0.96[CEU][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1056476	0.80[CHB][hapmap]
rs10867956	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10867958	0.83[EUR][1000 genomes]
rs11139953	0.84[ASN][1000 genomes]
rs11795061	0.85[ASN][1000 genomes]
rs12237222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1323765	0.84[ASN][1000 genomes]
rs1323766	0.84[ASN][1000 genomes]
rs1408102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1408103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1830772	0.84[ASN][1000 genomes]
rs7035425	0.80[CHB][hapmap]
rs7041473	0.84[ASN][1000 genomes]
rs7041613	0.84[ASN][1000 genomes]
rs7864580	0.84[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	nsv818710	chr9:85834312-85835108	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1408101	FRMD3	cis	Frontal Cortex	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:85833600-85834800	Active TSS	A549	lung
2	chr9:85833600-85835000	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr9:85833600-85835600	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr9:85833800-85834800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr9:85833800-85834800	Active TSS	NHEK	skin
6	chr9:85833800-85835000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr9:85833800-85835000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
8	chr9:85833800-85835000	Active TSS	Lung	lung
9	chr9:85833800-85835000	Active TSS	Pancreas	Pancrea
10	chr9:85833800-85835200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr9:85834000-85834400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr9:85834000-85834400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
13	chr9:85834000-85834400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
14	chr9:85834000-85834400	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
15	chr9:85834000-85834400	Flanking Active TSS	HMEC	breast
16	chr9:85834000-85834400	Active TSS	Monocytes-CD14+_RO01746	blood
17	chr9:85834000-85834600	Active TSS	HSMM	muscle
18	chr9:85834000-85834800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr9:85834000-85834800	Active TSS	Primary B cells from cord blood	blood
20	chr9:85834000-85834800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr9:85834000-85834800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr9:85834000-85834800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr9:85834000-85834800	Active TSS	Aorta	Aorta
24	chr9:85834000-85834800	Active TSS	Brain Angular Gyrus	brain
25	chr9:85834000-85834800	Active TSS	Brain Hippocampus Middle	brain
26	chr9:85834000-85834800	Active TSS	Duodenum Mucosa	Duodenum
27	chr9:85834000-85834800	Active TSS	Esophagus	oesophagus
28	chr9:85834000-85834800	Active TSS	Fetal Brain Female	brain
29	chr9:85834000-85834800	Active TSS	Fetal Lung	lung
30	chr9:85834000-85834800	Active TSS	Skeletal Muscle Female	skeletal muscle
31	chr9:85834000-85834800	Active TSS	HepG2	liver
32	chr9:85834000-85834800	Active TSS	NHDF-Ad	bronchial
33	chr9:85834000-85834800	Active TSS	Osteobl	bone
34	chr9:85834000-85835000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr9:85834000-85835000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr9:85834000-85835000	Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr9:85834000-85835000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
38	chr9:85834000-85835000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr9:85834000-85835000	Active TSS	Muscle Satellite Cultured Cells	--
40	chr9:85834000-85835000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr9:85834000-85835000	Active TSS	Brain Anterior Caudate	brain
42	chr9:85834000-85835000	Active TSS	Brain Cingulate Gyrus	brain
43	chr9:85834000-85835000	Active TSS	Fetal Intestine Large	intestine
44	chr9:85834000-85835000	Active TSS	Fetal Intestine Small	intestine
45	chr9:85834000-85835000	Active TSS	Fetal Kidney	kidney
46	chr9:85834000-85835000	Active TSS	Fetal Stomach	stomach
47	chr9:85834000-85835000	Active TSS	Left Ventricle	heart
48	chr9:85834000-85835000	Active TSS	Ovary	ovary
49	chr9:85834000-85835000	Active TSS	Psoas Muscle	Psoas
50	chr9:85834000-85835000	Active TSS	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links