Variant report

Variant	rs7162509
Chromosome Location	chr15:40863292-40863293
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:40855657..40859262-chr15:40860971..40863634,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128891	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10400825	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10467972	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11070284	0.86[EUR][1000 genomes]
rs11629680	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11637239	0.88[EUR][1000 genomes]
rs11854763	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12438955	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12440468	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12592882	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12708401	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12911738	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12912058	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12912339	0.86[EUR][1000 genomes]
rs12915109	0.84[EUR][1000 genomes]
rs12916082	0.84[EUR][1000 genomes]
rs1901775	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2278888	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2412541	0.86[EUR][1000 genomes]
rs3092978	0.86[EUR][1000 genomes]
rs4420508	0.86[EUR][1000 genomes]
rs4439732	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4924484	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4924487	0.86[EUR][1000 genomes]
rs4924488	0.86[EUR][1000 genomes]
rs4924491	0.82[EUR][1000 genomes]
rs55640412	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6492957	0.87[EUR][1000 genomes]
rs6492958	0.87[EUR][1000 genomes]
rs66885559	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7161938	0.87[EUR][1000 genomes]
rs7161968	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7162319	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7164289	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7167417	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7168873	0.82[EUR][1000 genomes]
rs7171260	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7171945	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7172947	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7176974	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7177192	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7178486	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72733486	0.85[EUR][1000 genomes]
rs8028999	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8031057	0.84[EUR][1000 genomes]
rs8035775	0.86[EUR][1000 genomes]
rs8037417	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8037804	0.86[EUR][1000 genomes]
rs8040502	0.86[EUR][1000 genomes]
rs8042729	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs896796	0.93[EUR][1000 genomes]
rs936580	0.81[EUR][1000 genomes]
rs9806221	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv832984	chr15:40794391-40998535	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	esv2758378	chr15:40832545-40995111	Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2760026	chr15:40832545-40995111	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7162509	RMDN3	cis	Muscle Skeletal	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40862200-40863400	Enhancers	Spleen	Spleen
2	chr15:40862400-40863600	Weak transcription	Gastric	stomach
3	chr15:40862400-40863800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr15:40862400-40863800	Weak transcription	Placenta	Placenta
5	chr15:40862400-40863800	Weak transcription	Lung	lung
6	chr15:40862400-40865600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr15:40862400-40865600	Weak transcription	Esophagus	oesophagus
8	chr15:40862600-40863800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr15:40862600-40863800	Weak transcription	Pancreas	Pancrea
10	chr15:40862600-40864000	Genic enhancers	Primary T cells fromperipheralblood	blood
11	chr15:40862600-40864000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr15:40862600-40864000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr15:40862600-40865600	Weak transcription	Left Ventricle	heart
14	chr15:40862800-40863600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr15:40862800-40863600	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr15:40862800-40863600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr15:40862800-40863600	Weak transcription	Ovary	ovary
18	chr15:40862800-40863800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr15:40862800-40863800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr15:40862800-40863800	Weak transcription	Thymus	Thymus
21	chr15:40862800-40864800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr15:40862800-40867000	Strong transcription	Fetal Muscle Trunk	muscle
23	chr15:40862800-40875200	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr15:40863000-40863400	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr15:40863000-40863600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr15:40863000-40863600	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr15:40863000-40863600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr15:40863000-40863600	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr15:40863000-40863600	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr15:40863000-40863600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr15:40863000-40863600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr15:40863000-40863600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr15:40863000-40863600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr15:40863000-40863600	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr15:40863000-40863600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr15:40863000-40863600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr15:40863000-40863600	Weak transcription	Adipose Nuclei	Adipose
38	chr15:40863000-40863600	Weak transcription	Brain Anterior Caudate	brain
39	chr15:40863000-40863600	Weak transcription	Brain Cingulate Gyrus	brain
40	chr15:40863000-40863600	Weak transcription	Fetal Kidney	kidney
41	chr15:40863000-40863600	Enhancers	HepG2	liver
42	chr15:40863000-40863600	Weak transcription	NHDF-Ad	bronchial
43	chr15:40863000-40863800	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr15:40863000-40863800	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr15:40863000-40863800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr15:40863000-40863800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr15:40863000-40863800	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr15:40863000-40863800	Weak transcription	Brain Germinal Matrix	brain
49	chr15:40863000-40863800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr15:40863000-40863800	Weak transcription	Duodenum Mucosa	Duodenum

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