Variant report

Variant	rs11638204
Chromosome Location	chr15:41000508-41000509
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	chr15:40998354..41000598-chr15:41004908..41006677,2	K562	blood:

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10400825	0.82[EUR][1000 genomes]
rs10744948	0.88[EUR][1000 genomes]
rs11070284	0.89[EUR][1000 genomes]
rs11070292	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1142468	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11561564	0.84[EUR][1000 genomes]
rs11633367	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11854763	0.89[EUR][1000 genomes]
rs12438182	0.83[EUR][1000 genomes]
rs12438955	0.89[EUR][1000 genomes]
rs12708401	0.89[EUR][1000 genomes]
rs12899600	0.85[EUR][1000 genomes]
rs12906095	0.84[EUR][1000 genomes]
rs12911738	0.89[EUR][1000 genomes]
rs12912058	0.89[EUR][1000 genomes]
rs12912339	0.89[EUR][1000 genomes]
rs2304580	0.96[EUR][1000 genomes]
rs2412541	0.89[EUR][1000 genomes]
rs2619681	0.99[EUR][1000 genomes]
rs3092978	0.89[EUR][1000 genomes]
rs34285050	0.99[EUR][1000 genomes]
rs4306472	0.82[EUR][1000 genomes]
rs4417527	0.99[EUR][1000 genomes]
rs4420508	0.89[EUR][1000 genomes]
rs45457497	0.95[EUR][1000 genomes]
rs4924484	0.88[EUR][1000 genomes]
rs4924487	0.89[EUR][1000 genomes]
rs4924488	0.89[EUR][1000 genomes]
rs4924490	0.83[EUR][1000 genomes]
rs4924491	0.93[EUR][1000 genomes]
rs4924500	0.99[EUR][1000 genomes]
rs62019923	0.83[EUR][1000 genomes]
rs62019925	0.83[EUR][1000 genomes]
rs6492957	0.82[EUR][1000 genomes]
rs6492958	0.82[EUR][1000 genomes]
rs7161938	0.82[EUR][1000 genomes]
rs7161968	0.82[EUR][1000 genomes]
rs7164289	0.83[EUR][1000 genomes]
rs7167417	0.89[EUR][1000 genomes]
rs7168873	0.85[EUR][1000 genomes]
rs7171260	0.89[EUR][1000 genomes]
rs7172947	0.82[EUR][1000 genomes]
rs7175361	0.90[EUR][1000 genomes]
rs7176221	0.82[EUR][1000 genomes]
rs7176974	0.89[EUR][1000 genomes]
rs7177192	0.89[EUR][1000 genomes]
rs7178486	0.89[EUR][1000 genomes]
rs8025008	0.93[EUR][1000 genomes]
rs8031057	0.87[EUR][1000 genomes]
rs8035775	0.89[EUR][1000 genomes]
rs8037804	0.89[EUR][1000 genomes]
rs8040502	0.89[EUR][1000 genomes]
rs8041443	0.81[EUR][1000 genomes]
rs936580	0.84[EUR][1000 genomes]
rs9806221	0.88[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	nsv529030	chr15:40956471-41012695	Active TSS Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	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
6	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
rs11638204	RMDN3	cis	Heart Left Ventricle	GTEx
rs11638204	RMDN3	cis	Muscle Skeletal	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40988000-41030000	Weak transcription	Pancreas	Pancrea
2	chr15:40988200-41001200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:40988200-41028600	Weak transcription	Spleen	Spleen
4	chr15:40988400-41020600	Weak transcription	Placenta	Placenta
5	chr15:40988400-41020800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr15:40988400-41021600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr15:40988400-41021800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr15:40988400-41027200	Weak transcription	Primary B cells from cord blood	blood
9	chr15:40988400-41031000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr15:40988600-41000800	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr15:40988600-41001200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr15:40988600-41007800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr15:40988600-41018400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr15:40988600-41021400	Weak transcription	Duodenum Mucosa	Duodenum
15	chr15:40988600-41021400	Weak transcription	Fetal Brain Female	brain
16	chr15:40988800-41000800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr15:40988800-41000800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr15:40988800-41000800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr15:40988800-41001200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr15:40988800-41002800	Weak transcription	Brain Germinal Matrix	brain
21	chr15:40988800-41020600	Weak transcription	Primary T cells from cord blood	blood
22	chr15:40988800-41021600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr15:40988800-41021800	Weak transcription	Fetal Kidney	kidney
24	chr15:40989000-41001000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr15:40989000-41001200	Weak transcription	Fetal Lung	lung
26	chr15:40989000-41012000	Weak transcription	NHLF	lung
27	chr15:40989000-41018000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr15:40989200-41001200	Weak transcription	A549	lung
29	chr15:40989200-41002800	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr15:40990000-41004800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr15:40990200-41006800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr15:40990200-41013200	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr15:40990200-41016800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr15:40990200-41016800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr15:40990600-41015000	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr15:40990600-41022600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr15:40990800-41005000	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr15:40990800-41005200	Strong transcription	Fetal Thymus	thymus
39	chr15:40990800-41005400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr15:40990800-41016000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr15:40991000-41007200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr15:40992000-41001600	Weak transcription	Esophagus	oesophagus
43	chr15:40992000-41016600	Strong transcription	Dnd41	blood
44	chr15:40992400-41000800	Weak transcription	Fetal Muscle Leg	muscle
45	chr15:40992600-41001000	Weak transcription	NH-A	brain
46	chr15:40992800-41006200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr15:40993200-41025800	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr15:40993400-41000800	Weak transcription	HepG2	liver
49	chr15:40993600-41001000	Weak transcription	Primary hematopoietic stem cells	blood
50	chr15:40994000-41001000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links