Variant report

Variant	rs12438955
Chromosome Location	chr15:40890510-40890511
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:40885453..40889307-chr15:40890037..40892852,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137812	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10400825	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10467972	0.85[EUR][1000 genomes]
rs10744948	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11070284	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1142468	0.84[EUR][1000 genomes]
rs11561564	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11629680	0.83[EUR][1000 genomes]
rs11633367	0.83[EUR][1000 genomes]
rs11638204	0.89[EUR][1000 genomes]
rs11854763	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12440468	0.85[EUR][1000 genomes]
rs12592882	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12708401	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12899600	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12906095	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12911738	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12912058	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12912339	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12915109	0.89[EUR][1000 genomes]
rs12916082	0.89[EUR][1000 genomes]
rs1901775	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2278888	0.85[EUR][1000 genomes]
rs2304580	0.87[EUR][1000 genomes]
rs2412541	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2619681	0.90[EUR][1000 genomes]
rs3092978	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34285050	0.90[EUR][1000 genomes]
rs4306472	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4417527	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4420508	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4439732	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs45457497	0.87[EUR][1000 genomes]
rs4924484	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924487	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4924488	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4924490	0.83[EUR][1000 genomes]
rs4924491	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4924500	0.90[EUR][1000 genomes]
rs55640412	0.85[EUR][1000 genomes]
rs62019923	0.85[EUR][1000 genomes]
rs62019925	0.85[EUR][1000 genomes]
rs6492956	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6492957	0.92[EUR][1000 genomes]
rs6492958	0.92[EUR][1000 genomes]
rs66885559	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7161938	0.92[EUR][1000 genomes]
rs7161968	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7162319	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7162509	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7164289	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7167417	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7167768	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7168873	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7171260	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7171945	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7172947	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7175361	0.84[EUR][1000 genomes]
rs7176221	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7176974	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7177192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7178486	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8025008	0.85[EUR][1000 genomes]
rs8028999	0.85[EUR][1000 genomes]
rs8031057	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8035775	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8037417	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8037804	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8040502	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8041095	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs8041443	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs896796	0.82[EUR][1000 genomes]
rs936580	0.95[EUR][1000 genomes]
rs9806221	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12438955	RMDN3	cis	Heart Left Ventricle	GTEx
rs12438955	RMDN3	cis	Muscle Skeletal	GTEx

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40887200-40893200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:40887200-40898800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr15:40887400-40891600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr15:40887600-40898800	Weak transcription	Fetal Muscle Trunk	muscle
5	chr15:40887600-40902600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr15:40887600-40941800	Weak transcription	Fetal Intestine Large	intestine
7	chr15:40887800-40895400	Weak transcription	Fetal Muscle Leg	muscle
8	chr15:40887800-40898800	Weak transcription	Fetal Stomach	stomach
9	chr15:40887800-40902000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr15:40887800-40933200	Weak transcription	Duodenum Mucosa	Duodenum
11	chr15:40887800-40942200	Weak transcription	Primary B cells from cord blood	blood
12	chr15:40887800-40948200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr15:40887800-40961600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr15:40888000-40892800	Weak transcription	Fetal Heart	heart
15	chr15:40888000-40895000	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr15:40888000-40895800	Weak transcription	Thymus	Thymus
17	chr15:40888000-40897800	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr15:40888000-40898000	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr15:40888000-40898600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr15:40888000-40899400	Weak transcription	HSMM	muscle
21	chr15:40888000-40901200	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr15:40888000-40903400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr15:40888000-40956000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr15:40888200-40897800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr15:40888200-40898600	Weak transcription	Primary hematopoietic stem cells	blood
26	chr15:40888200-40898800	Weak transcription	NH-A	brain
27	chr15:40888200-40902200	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr15:40888200-40912800	Weak transcription	HMEC	breast
29	chr15:40888400-40892800	Weak transcription	Brain Germinal Matrix	brain
30	chr15:40888400-40895800	Weak transcription	Fetal Thymus	thymus
31	chr15:40888400-40897800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr15:40888400-40898000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr15:40888400-40898200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr15:40888400-40898800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr15:40888400-40898800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr15:40888400-40898800	Weak transcription	Fetal Intestine Small	intestine
37	chr15:40888400-40899800	Weak transcription	HUVEC	blood vessel
38	chr15:40888400-40900800	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr15:40888400-40913200	Weak transcription	NHDF-Ad	bronchial
40	chr15:40888400-40913600	Weak transcription	NHLF	lung
41	chr15:40888400-40923200	Weak transcription	Osteobl	bone
42	chr15:40888400-40925800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr15:40888400-40944200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr15:40889600-40895200	Weak transcription	Hela-S3	cervix
45	chr15:40889600-40898000	Weak transcription	K562	blood
46	chr15:40889600-40901400	Weak transcription	HepG2	liver
47	chr15:40889800-40890800	Enhancers	A549	lung
48	chr15:40889800-40893000	Weak transcription	GM12878-XiMat	blood
49	chr15:40890000-40890600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr15:40890200-40890800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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