Variant report

Variant	rs1408103
Chromosome Location	chr9:85834617-85834618
allele	A/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	chr9:85834525..85835178-chr9:86153175..86154166,3	MCF-7	breast:
7	chr9:85832727..85836639-chr9:86319596..86323973,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135018	Chromatin interaction
ENSG00000172159	Chromatin interaction
ENSG00000254473	Chromatin interaction
ENSG00000251776	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10125314	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10867956	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10867958	0.80[AMR][1000 genomes];0.84[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];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1323765	0.84[ASN][1000 genomes]
rs1323766	0.84[ASN][1000 genomes]
rs1408101	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]
rs1408102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1830772	0.84[ASN][1000 genomes]
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
rs1408103	FRMD3	cis	Frontal Cortex	GTEx

Chromatin state (count:115 , 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	chr9:85834000-85834800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr9:85834000-85834800	Active TSS	Primary B cells from cord blood	blood
13	chr9:85834000-85834800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr9:85834000-85834800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr9:85834000-85834800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr9:85834000-85834800	Active TSS	Aorta	Aorta
17	chr9:85834000-85834800	Active TSS	Brain Angular Gyrus	brain
18	chr9:85834000-85834800	Active TSS	Brain Hippocampus Middle	brain
19	chr9:85834000-85834800	Active TSS	Duodenum Mucosa	Duodenum
20	chr9:85834000-85834800	Active TSS	Esophagus	oesophagus
21	chr9:85834000-85834800	Active TSS	Fetal Brain Female	brain
22	chr9:85834000-85834800	Active TSS	Fetal Lung	lung
23	chr9:85834000-85834800	Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr9:85834000-85834800	Active TSS	HepG2	liver
25	chr9:85834000-85834800	Active TSS	NHDF-Ad	bronchial
26	chr9:85834000-85834800	Active TSS	Osteobl	bone
27	chr9:85834000-85835000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr9:85834000-85835000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr9:85834000-85835000	Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr9:85834000-85835000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
31	chr9:85834000-85835000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr9:85834000-85835000	Active TSS	Muscle Satellite Cultured Cells	--
33	chr9:85834000-85835000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr9:85834000-85835000	Active TSS	Brain Anterior Caudate	brain
35	chr9:85834000-85835000	Active TSS	Brain Cingulate Gyrus	brain
36	chr9:85834000-85835000	Active TSS	Fetal Intestine Large	intestine
37	chr9:85834000-85835000	Active TSS	Fetal Intestine Small	intestine
38	chr9:85834000-85835000	Active TSS	Fetal Kidney	kidney
39	chr9:85834000-85835000	Active TSS	Fetal Stomach	stomach
40	chr9:85834000-85835000	Active TSS	Left Ventricle	heart
41	chr9:85834000-85835000	Active TSS	Ovary	ovary
42	chr9:85834000-85835000	Active TSS	Psoas Muscle	Psoas
43	chr9:85834000-85835000	Active TSS	Rectal Mucosa Donor 29	rectum
44	chr9:85834000-85835000	Active TSS	Rectal Smooth Muscle	rectum
45	chr9:85834000-85835000	Active TSS	Right Atrium	heart
46	chr9:85834000-85835000	Active TSS	Right Ventricle	heart
47	chr9:85834000-85835000	Active TSS	HSMMtube	muscle
48	chr9:85834000-85835200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr9:85834000-85835200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr9:85834000-85835200	Flanking Active TSS	Adipose Nuclei	Adipose

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