Variant report

Variant	rs8041443
Chromosome Location	chr15:40939652-40939653
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr15:40939573-40940291	GM12878	blood:	n/a	chr15:40939913-40939928

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:40938971..40941359-chr15:40954270..40956007,2	MCF-7	breast:
2	chr15:40886178..40888250-chr15:40939361..40941030,2	K562	blood:

Variant related genes	Relation type
CASC5	TF binding region
ENSG00000137812	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10400825	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10744948	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11070284	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11561564	0.91[AMR][1000 genomes]
rs11638204	0.81[EUR][1000 genomes]
rs11854763	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12438955	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12592882	0.81[ASN][1000 genomes]
rs12708401	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12899600	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12906095	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12911738	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12912058	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12912339	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12915109	0.81[EUR][1000 genomes]
rs12916082	0.81[EUR][1000 genomes]
rs2412541	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2619681	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3092978	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34285050	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4306472	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4417527	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4420508	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs45457497	0.86[ASN][1000 genomes]
rs4924484	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4924487	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4924488	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4924491	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4924500	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62019923	0.90[AMR][1000 genomes]
rs62019924	0.89[AMR][1000 genomes]
rs62019925	0.89[AMR][1000 genomes]
rs6492957	0.84[EUR][1000 genomes]
rs6492958	0.84[EUR][1000 genomes]
rs66885559	0.81[ASN][1000 genomes]
rs7161938	0.84[EUR][1000 genomes]
rs7161968	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7164289	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7167417	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7167768	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7168873	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7171260	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7171945	0.80[ASN][1000 genomes]
rs7172947	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7175361	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7176221	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7176974	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7177192	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7178486	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8025008	0.83[ASN][1000 genomes]
rs8031057	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8035775	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8037417	0.80[ASN][1000 genomes]
rs8037804	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8040502	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8041095	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs936580	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9806221	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][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	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
4	esv1841263	chr15:40902453-40966765	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	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
6	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs8041443	RMDN3	cis	Muscle Skeletal	GTEx
rs8041443	RMDN3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40887600-40941800	Weak transcription	Fetal Intestine Large	intestine
2	chr15:40887800-40942200	Weak transcription	Primary B cells from cord blood	blood
3	chr15:40887800-40948200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr15:40887800-40961600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr15:40888000-40956000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr15:40888400-40944200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr15:40897800-40957200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:40900000-40943600	Weak transcription	NH-A	brain
9	chr15:40903000-40956000	Weak transcription	Fetal Heart	heart
10	chr15:40903600-40956600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:40903800-40955800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr15:40903800-40956600	Weak transcription	Fetal Lung	lung
13	chr15:40912200-40951400	Weak transcription	Fetal Kidney	kidney
14	chr15:40912600-40941400	Weak transcription	HepG2	liver
15	chr15:40913800-40986000	Weak transcription	A549	lung
16	chr15:40914400-40960000	Weak transcription	NHLF	lung
17	chr15:40914800-40942600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr15:40919200-40957600	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr15:40919400-40956800	Strong transcription	Fetal Thymus	thymus
20	chr15:40919800-40950200	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr15:40922600-40943800	Weak transcription	Hela-S3	cervix
22	chr15:40922800-40944000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr15:40922800-40944000	Weak transcription	NHEK	skin
24	chr15:40922800-40954200	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr15:40922800-40956000	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr15:40923000-40954400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr15:40923200-40947000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr15:40924000-40956600	Weak transcription	Fetal Brain Female	brain
29	chr15:40924400-40943600	Weak transcription	Osteobl	bone
30	chr15:40925000-40956200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr15:40925400-40956000	Weak transcription	Brain Germinal Matrix	brain
32	chr15:40926000-40947200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr15:40926000-40958800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr15:40927200-40942000	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr15:40928200-40949400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr15:40928200-40951200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr15:40928600-40945600	Weak transcription	Fetal Muscle Leg	muscle
38	chr15:40928600-40958000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr15:40931400-40944200	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr15:40932200-40941800	Weak transcription	Fetal Intestine Small	intestine
41	chr15:40932600-40946800	Weak transcription	Fetal Stomach	stomach
42	chr15:40933800-40941800	Weak transcription	Duodenum Mucosa	Duodenum
43	chr15:40934000-40942400	Weak transcription	NHDF-Ad	bronchial
44	chr15:40934200-40942600	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr15:40934200-40942800	Weak transcription	HMEC	breast
46	chr15:40934200-40945000	Weak transcription	HSMM	muscle
47	chr15:40934200-40949400	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr15:40935200-40942600	Weak transcription	K562	blood
49	chr15:40936000-40942600	Weak transcription	GM12878-XiMat	blood
50	chr15:40936200-40942000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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