Variant report

Variant	rs2219889
Chromosome Location	chr15:83613169-83613170
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83611228..83613735-chr15:83667947..83669649,2	MCF-7	breast:
2	chr15:83612419..83614260-chr15:83631373..83634308,2	MCF-7	breast:
3	chr15:83558429..83560638-chr15:83611658..83613627,2	MCF-7	breast:
4	chr15:83254004..83256301-chr15:83611241..83613482,2	MCF-7	breast:
5	chr15:83611625..83613559-chr15:83679581..83681171,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169609	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs17294476	0.98[ASN][1000 genomes]
rs55754542	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs58070122	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs60490665	0.81[AFR][1000 genomes]

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	nsv1040336	chr15:83578947-83768335	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv482308	chr15:83584918-83747362	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2219889	FAM103A1	cis	Skin Sun Exposed Lower leg	GTEx
rs2219889	FAM103A1	cis	lung	GTEx
rs2219889	FAM103A1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83586600-83619400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr15:83606600-83613200	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr15:83606600-83618800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr15:83606600-83620000	Weak transcription	Right Ventricle	heart
5	chr15:83609000-83613800	Enhancers	Pancreas	Pancrea
6	chr15:83610600-83613800	Enhancers	Gastric	stomach
7	chr15:83610600-83614200	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr15:83611200-83614400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr15:83611400-83619800	Weak transcription	Esophagus	oesophagus
10	chr15:83611800-83620400	Weak transcription	Right Atrium	heart
11	chr15:83612000-83613200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr15:83612000-83613400	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr15:83612200-83613200	Weak transcription	HSMM	muscle
14	chr15:83612200-83613600	Weak transcription	Left Ventricle	heart
15	chr15:83612200-83614000	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr15:83612200-83617800	Weak transcription	Lung	lung
17	chr15:83612200-83618200	Weak transcription	Liver	Liver
18	chr15:83612200-83619200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr15:83612200-83619800	Weak transcription	HSMMtube	muscle
20	chr15:83612400-83613200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr15:83612400-83613400	Enhancers	Psoas Muscle	Psoas
22	chr15:83612600-83613400	Enhancers	Brain Substantia Nigra	brain
23	chr15:83612600-83613800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr15:83612600-83617800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr15:83612600-83619800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr15:83612800-83613200	Weak transcription	Brain Anterior Caudate	brain
27	chr15:83613000-83613400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr15:83613000-83613600	Enhancers	Fetal Brain Male	brain
29	chr15:83613000-83613800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr15:83613000-83614000	Enhancers	Primary B cells from peripheral blood	blood

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