Variant report

Variant	rs7162319
Chromosome Location	chr15:40862470-40862471
allele	C/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:
2	chr15:40860821..40863087-chr15:40987318..40989233,3	K562	blood:

Variant related genes	Relation type
ENSG00000051180	Chromatin interaction
ENSG00000128891	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10400825	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10467972	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11070284	0.84[EUR][1000 genomes]
rs11629680	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11637239	0.88[EUR][1000 genomes]
rs11854763	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12438955	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12440468	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12592882	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12708401	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12911738	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12912058	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12912339	0.84[EUR][1000 genomes]
rs12915109	0.81[EUR][1000 genomes]
rs12916082	0.81[EUR][1000 genomes]
rs1901775	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2278888	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2412541	0.84[EUR][1000 genomes]
rs3092978	0.84[EUR][1000 genomes]
rs4420508	0.84[EUR][1000 genomes]
rs4439732	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4924484	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4924487	0.84[EUR][1000 genomes]
rs4924488	0.84[EUR][1000 genomes]
rs55640412	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6492957	0.84[EUR][1000 genomes]
rs6492958	0.84[EUR][1000 genomes]
rs66885559	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7161938	0.84[EUR][1000 genomes]
rs7161968	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7162509	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7164289	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7167417	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7168873	0.80[EUR][1000 genomes]
rs7171260	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7171945	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7172947	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7176974	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7177192	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7178486	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72733486	0.85[EUR][1000 genomes]
rs8028999	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8031057	0.82[EUR][1000 genomes]
rs8035775	0.84[EUR][1000 genomes]
rs8037417	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8037804	0.84[EUR][1000 genomes]
rs8040502	0.84[EUR][1000 genomes]
rs8042729	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs896796	0.93[EUR][1000 genomes]
rs9806221	0.83[EUR][1000 genomes];0.87[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
rs7162319	RMDN3	cis	Muscle Skeletal	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40860800-40862600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr15:40860800-40863200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr15:40861000-40862600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr15:40861000-40862600	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr15:40861000-40862600	Flanking Active TSS	Primary hematopoietic stem cells	blood
6	chr15:40861000-40862600	Active TSS	Psoas Muscle	Psoas
7	chr15:40861000-40862600	Active TSS	NHDF-Ad	bronchial
8	chr15:40861000-40862800	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr15:40861000-40862800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr15:40861000-40862800	Active TSS	Right Atrium	heart
11	chr15:40861000-40863000	Active TSS	H1 Cell Line	embryonic stem cell
12	chr15:40861000-40863000	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr15:40861000-40863200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr15:40861200-40862600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:40861200-40862600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr15:40861200-40862600	Active TSS	Left Ventricle	heart
17	chr15:40861200-40862600	Active TSS	GM12878-XiMat	blood
18	chr15:40861200-40862800	Active TSS	H9 Cell Line	embryonic stem cell
19	chr15:40861400-40862600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr15:40861400-40862600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr15:40861400-40862600	Active TSS	HSMM	muscle
22	chr15:40861800-40862600	Flanking Active TSS	Primary B cells from cord blood	blood
23	chr15:40861800-40862800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr15:40861800-40863000	Flanking Active TSS	Adipose Nuclei	Adipose
25	chr15:40862000-40862600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
26	chr15:40862000-40862600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
27	chr15:40862000-40862600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
28	chr15:40862000-40862600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
29	chr15:40862000-40862600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr15:40862000-40862600	Flanking Active TSS	Liver	Liver
31	chr15:40862000-40862600	Flanking Active TSS	Brain Hippocampus Middle	brain
32	chr15:40862000-40862600	Flanking Active TSS	Fetal Muscle Leg	muscle
33	chr15:40862000-40862800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr15:40862000-40862800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
35	chr15:40862000-40863000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
36	chr15:40862000-40863200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
37	chr15:40862000-40863200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr15:40862200-40862600	Flanking Active TSS	Primary B cells from peripheral blood	blood
39	chr15:40862200-40862600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
40	chr15:40862200-40862600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr15:40862200-40862600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
42	chr15:40862200-40862600	Flanking Active TSS	Brain Substantia Nigra	brain
43	chr15:40862200-40862600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
44	chr15:40862200-40862600	Flanking Active TSS	Fetal Heart	heart
45	chr15:40862200-40862600	Flanking Active TSS	Fetal Stomach	stomach
46	chr15:40862200-40862600	Flanking Active TSS	Fetal Thymus	thymus
47	chr15:40862200-40862600	Flanking Active TSS	Placenta Amnion	Placenta Amnion
48	chr15:40862200-40862600	Flanking Active TSS	Stomach Mucosa	stomach
49	chr15:40862200-40862800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
50	chr15:40862200-40862800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin

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