Variant report

Variant	rs4924500
Chromosome Location	chr15:41015751-41015752
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:40986444..40988095-chr15:41015156..41017293,3	K562	blood:

Variant related genes	Relation type
ENSG00000245849	Chromatin interaction
ENSG00000051180	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10400825	0.83[EUR][1000 genomes]
rs10467972	0.89[CEU][hapmap];0.94[JPT][hapmap]
rs10744948	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11070284	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11070292	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs1142468	0.89[EUR][1000 genomes]
rs11561564	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11633367	0.90[EUR][1000 genomes]
rs11638204	0.99[EUR][1000 genomes]
rs11854763	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11858338	0.81[YRI][hapmap]
rs12438182	0.82[EUR][1000 genomes]
rs12438955	0.90[EUR][1000 genomes]
rs12708401	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12899600	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12906095	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12911738	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12912058	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12912339	0.84[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];0.94[JPT][hapmap]
rs2304580	1.00[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2304582	0.80[YRI][hapmap]
rs2412541	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2619681	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3092978	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3092982	0.86[YRI][hapmap]
rs34285050	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4306472	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4417527	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]
rs4420508	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs45457497	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924484	0.89[EUR][1000 genomes]
rs4924487	1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4924488	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4924490	0.82[EUR][1000 genomes]
rs4924491	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62019923	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62019924	0.80[AMR][1000 genomes]
rs62019925	0.80[AMR][1000 genomes];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];0.93[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.90[EUR][1000 genomes]
rs7168873	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7171260	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7172947	0.83[EUR][1000 genomes]
rs7175361	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7176221	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7176974	0.90[EUR][1000 genomes]
rs7177192	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7178486	0.90[EUR][1000 genomes]
rs8025008	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8028999	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs8031057	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8035775	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8037804	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8040502	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];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	0.88[CEU][hapmap];0.94[JPT][hapmap]
rs896796	1.00[CEU][hapmap]
rs936580	0.85[EUR][1000 genomes]
rs9806221	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4924500	RMDN3	cis	Heart Left Ventricle	GTEx
rs4924500	RMDN3	cis	Muscle Skeletal	GTEx

Chromatin state (count:88 , 50 per page) page: 1 2

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	chr15:40988400-41020600	Weak transcription	Placenta	Placenta
4	chr15:40988400-41020800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr15:40988400-41021600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr15:40988400-41021800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr15:40988400-41027200	Weak transcription	Primary B cells from cord blood	blood
8	chr15:40988400-41031000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr15:40988600-41018400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr15:40988600-41021400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr15:40988600-41021400	Weak transcription	Fetal Brain Female	brain
12	chr15:40988800-41020600	Weak transcription	Primary T cells from cord blood	blood
13	chr15:40988800-41021600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr15:40988800-41021800	Weak transcription	Fetal Kidney	kidney
15	chr15:40989000-41018000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:40990200-41016800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr15:40990200-41016800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr15:40990600-41022600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr15:40990800-41016000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr15:40992000-41016600	Strong transcription	Dnd41	blood
21	chr15:40993200-41025800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr15:40994000-41020600	Weak transcription	HSMM	muscle
23	chr15:40997800-41020800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr15:40998200-41023200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr15:40998800-41038000	Weak transcription	Stomach Mucosa	stomach
26	chr15:40999000-41027600	Weak transcription	Gastric	stomach
27	chr15:40999200-41021600	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr15:41000000-41026000	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr15:41001400-41020800	Weak transcription	NHDF-Ad	bronchial
30	chr15:41001600-41020600	Weak transcription	NH-A	brain
31	chr15:41002000-41019600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr15:41002000-41021400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr15:41002200-41021600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr15:41002800-41019400	Weak transcription	Fetal Stomach	stomach
35	chr15:41003200-41021800	Weak transcription	Brain Germinal Matrix	brain
36	chr15:41003600-41021800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr15:41003800-41023800	Weak transcription	Fetal Lung	lung
38	chr15:41004000-41021600	Weak transcription	Osteobl	bone
39	chr15:41004600-41021000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr15:41004800-41020600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr15:41004800-41022000	Weak transcription	A549	lung
42	chr15:41004800-41023400	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr15:41005000-41019600	Weak transcription	Primary hematopoietic stem cells	blood
44	chr15:41005000-41021400	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr15:41005800-41016600	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr15:41006400-41021800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr15:41007200-41020600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr15:41007400-41020800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr15:41008200-41046600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr15:41009800-41016400	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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