Variant report

Variant	rs1901775
Chromosome Location	chr15:40874660-40874661
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	chr15:40866258..40868658-chr15:40873477..40876647,3	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10400825	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10467972	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11070284	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11629680	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11637239	0.89[EUR][1000 genomes]
rs11854763	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12438955	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12440468	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12592882	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12708401	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12899600	0.81[EUR][1000 genomes]
rs12911738	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12912058	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12912339	0.87[EUR][1000 genomes]
rs12915109	0.85[EUR][1000 genomes]
rs12916082	0.85[EUR][1000 genomes]
rs2278888	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2412541	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3092978	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4306472	0.80[ASN][1000 genomes]
rs4420508	0.87[EUR][1000 genomes]
rs4439732	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4924484	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4924487	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4924488	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4924491	0.83[EUR][1000 genomes]
rs55640412	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6492957	0.88[EUR][1000 genomes]
rs6492958	0.88[EUR][1000 genomes]
rs66885559	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7161938	0.88[EUR][1000 genomes]
rs7161968	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7162319	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7162509	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7164289	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7167417	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7168873	0.83[EUR][1000 genomes]
rs7171260	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7171945	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7172947	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7176974	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7177192	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7178486	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72733486	0.86[EUR][1000 genomes]
rs8028999	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8031057	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8035775	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8037417	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8037804	0.87[EUR][1000 genomes]
rs8040502	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8042729	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs896796	0.94[EUR][1000 genomes]
rs936580	0.82[EUR][1000 genomes]
rs9806221	0.86[EUR][1000 genomes];0.90[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
rs1901775	RMDN3	cis	Muscle Skeletal	GTEx

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40862800-40875200	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr15:40863000-40875000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr15:40863000-40875000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr15:40865800-40875000	Weak transcription	Fetal Lung	lung
5	chr15:40866000-40874800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr15:40866400-40874800	Weak transcription	Colonic Mucosa	Colon
7	chr15:40866400-40876600	Weak transcription	HSMMtube	muscle
8	chr15:40866400-40878200	Weak transcription	Brain Angular Gyrus	brain
9	chr15:40866600-40874800	Weak transcription	Pancreas	Pancrea
10	chr15:40866600-40874800	Weak transcription	A549	lung
11	chr15:40866600-40875000	Weak transcription	Lung	lung
12	chr15:40866600-40875000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr15:40866600-40875200	Weak transcription	Spleen	Spleen
14	chr15:40866600-40875200	Weak transcription	HSMM	muscle
15	chr15:40866600-40881800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr15:40866600-40881800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr15:40866600-40881800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr15:40866800-40874800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr15:40866800-40875200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr15:40866800-40875200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr15:40866800-40875200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr15:40867000-40874800	Weak transcription	Osteobl	bone
23	chr15:40867000-40875200	Weak transcription	Fetal Muscle Trunk	muscle
24	chr15:40867200-40874800	Weak transcription	Brain Anterior Caudate	brain
25	chr15:40867200-40874800	Weak transcription	Fetal Muscle Leg	muscle
26	chr15:40867200-40875000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr15:40867200-40875000	Weak transcription	Primary B cells from cord blood	blood
28	chr15:40867200-40875000	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr15:40867200-40875000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr15:40867200-40875000	Weak transcription	Brain Substantia Nigra	brain
31	chr15:40867200-40875000	Weak transcription	Colon Smooth Muscle	Colon
32	chr15:40867200-40875000	Weak transcription	Stomach Smooth Muscle	stomach
33	chr15:40867200-40875200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr15:40867200-40875200	Weak transcription	Fetal Thymus	thymus
35	chr15:40867200-40875200	Weak transcription	Left Ventricle	heart
36	chr15:40867200-40875200	Weak transcription	HMEC	breast
37	chr15:40867200-40876400	Weak transcription	Brain Cingulate Gyrus	brain
38	chr15:40867400-40874800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr15:40867400-40874800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr15:40867400-40874800	Weak transcription	Placenta	Placenta
41	chr15:40867400-40874800	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr15:40867400-40875000	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr15:40867400-40875000	Weak transcription	Dnd41	blood
44	chr15:40867400-40875000	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr15:40867400-40875200	Weak transcription	Fetal Intestine Large	intestine
46	chr15:40867400-40875200	Weak transcription	NHDF-Ad	bronchial
47	chr15:40867400-40875400	Weak transcription	NHEK	skin
48	chr15:40867400-40876400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr15:40867400-40883600	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr15:40867600-40874800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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