Variant report

Variant	rs4417527
Chromosome Location	chr15:41021280-41021281
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:40992580..40995462-chr15:41019256..41021826,2	K562	blood:

Variant related genes	Relation type
ENSG00000051180	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10400825	0.83[EUR][1000 genomes]
rs10467972	0.91[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap]
rs10744948	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11070284	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11070292	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs1142468	0.89[EUR][1000 genomes]
rs11561564	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11633367	0.90[EUR][1000 genomes]
rs11638204	0.99[EUR][1000 genomes]
rs11854763	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12438182	0.82[EUR][1000 genomes]
rs12438955	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12708401	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12899600	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12906095	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12911738	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12912058	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12912339	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12915109	0.80[EUR][1000 genomes]
rs12916082	0.80[EUR][1000 genomes]
rs17747351	1.00[CEU][hapmap]
rs2278888	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap]
rs2304580	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2412541	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2619681	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3092978	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3092982	0.85[YRI][hapmap]
rs34285050	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4306472	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4420508	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs45457497	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924484	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4924487	0.91[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4924488	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4924490	0.82[EUR][1000 genomes]
rs4924491	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4924500	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62019923	0.84[EUR][1000 genomes]
rs62019925	0.84[EUR][1000 genomes]
rs6492957	0.83[EUR][1000 genomes]
rs6492958	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7161938	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7161968	0.83[EUR][1000 genomes]
rs7164289	0.84[EUR][1000 genomes]
rs7167417	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7168873	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7171260	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7172947	0.83[EUR][1000 genomes]
rs7175361	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7176221	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7176974	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7177192	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7178486	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8025008	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8028999	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap]
rs8031057	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8035775	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8037804	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8040502	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8041095	0.84[ASN][1000 genomes]
rs8041443	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8042729	0.90[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap]
rs896796	1.00[CEU][hapmap]
rs936580	0.85[EUR][1000 genomes]
rs9806221	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053173	chr15:40933163-41094127	Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv542363	chr15:40933163-41094127	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv904099	chr15:40949526-41041875	Genic enhancers Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
5	nsv527234	chr15:40987725-41031686	Transcr. at gene 5' and 3' Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	esv1819092	chr15:41017682-41255750	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4417527	RMDN3	cis	Muscle Skeletal	GTEx
rs4417527	RMDN3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40988000-41030000	Weak transcription	Pancreas	Pancrea
2	chr15:40988200-41028600	Weak transcription	Spleen	Spleen
3	chr15:40988400-41021600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr15:40988400-41021800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr15:40988400-41027200	Weak transcription	Primary B cells from cord blood	blood
6	chr15:40988400-41031000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr15:40988600-41021400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr15:40988600-41021400	Weak transcription	Fetal Brain Female	brain
9	chr15:40988800-41021600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr15:40988800-41021800	Weak transcription	Fetal Kidney	kidney
11	chr15:40990600-41022600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr15:40993200-41025800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr15:40998200-41023200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr15:40998800-41038000	Weak transcription	Stomach Mucosa	stomach
15	chr15:40999000-41027600	Weak transcription	Gastric	stomach
16	chr15:40999200-41021600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr15:41000000-41026000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr15:41002000-41021400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr15:41002200-41021600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr15:41003200-41021800	Weak transcription	Brain Germinal Matrix	brain
21	chr15:41003600-41021800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr15:41003800-41023800	Weak transcription	Fetal Lung	lung
23	chr15:41004000-41021600	Weak transcription	Osteobl	bone
24	chr15:41004800-41022000	Weak transcription	A549	lung
25	chr15:41004800-41023400	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr15:41005000-41021400	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr15:41006400-41021800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr15:41008200-41046600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr15:41010400-41021800	Weak transcription	HSMMtube	muscle
30	chr15:41010800-41021600	Weak transcription	Stomach Smooth Muscle	stomach
31	chr15:41011200-41021400	Weak transcription	Thymus	Thymus
32	chr15:41011200-41021600	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr15:41011200-41021800	Weak transcription	GM12878-XiMat	blood
34	chr15:41011400-41021600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr15:41012800-41021600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr15:41012800-41021600	Weak transcription	Fetal Intestine Large	intestine
37	chr15:41012800-41023600	Weak transcription	Brain Substantia Nigra	brain
38	chr15:41012800-41028200	Weak transcription	NHLF	lung
39	chr15:41014200-41021600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr15:41014200-41022200	Weak transcription	HUVEC	blood vessel
41	chr15:41014600-41029600	Weak transcription	Esophagus	oesophagus
42	chr15:41016600-41027400	Weak transcription	Brain Cingulate Gyrus	brain
43	chr15:41016800-41021800	Weak transcription	HMEC	breast
44	chr15:41018800-41021600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr15:41018800-41024800	Weak transcription	Primary B cells from peripheral blood	blood
46	chr15:41019000-41023800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr15:41019200-41021600	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr15:41019200-41023600	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr15:41019200-41035600	Weak transcription	Fetal Heart	heart
50	chr15:41019400-41024600	Weak transcription	Skeletal Muscle Male	skeletal muscle

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