Variant report

Variant	rs9847024
Chromosome Location	chr3:52959537-52959538
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs11130332	0.93[EUR][1000 genomes]
rs1134546	0.89[EUR][1000 genomes]
rs11707576	0.92[EUR][1000 genomes]
rs11708223	0.93[EUR][1000 genomes]
rs13082061	0.94[EUR][1000 genomes]
rs17304995	0.83[EUR][1000 genomes]
rs2246556	0.81[EUR][1000 genomes]
rs2336162	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2336666	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2336669	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2336671	0.89[EUR][1000 genomes]
rs2564947	0.88[EUR][1000 genomes]
rs2581779	0.87[EUR][1000 genomes]
rs2581780	0.87[EUR][1000 genomes]
rs2581796	0.87[EUR][1000 genomes]
rs2581797	0.93[EUR][1000 genomes]
rs2581801	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2581802	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2581805	0.93[EUR][1000 genomes]
rs2581810	0.97[EUR][1000 genomes]
rs2581815	0.93[EUR][1000 genomes]
rs2581820	0.91[EUR][1000 genomes]
rs2581823	0.90[EUR][1000 genomes]
rs2710342	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2710345	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2878762	0.88[AMR][1000 genomes]
rs34230854	0.83[EUR][1000 genomes]
rs35380116	0.91[EUR][1000 genomes]
rs4302374	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4519686	0.92[EUR][1000 genomes]
rs4687559	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4687560	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4687692	0.88[EUR][1000 genomes]
rs59989280	0.81[EUR][1000 genomes]
rs6445547	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6445550	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6768844	0.92[EUR][1000 genomes]
rs6770957	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6771610	0.91[EUR][1000 genomes]
rs6773040	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6789219	0.81[EUR][1000 genomes]
rs6792578	0.92[EUR][1000 genomes]
rs6797399	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6805298	0.81[EUR][1000 genomes]
rs71301803	0.83[EUR][1000 genomes]
rs71301807	0.84[EUR][1000 genomes]
rs7621939	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7644973	0.84[EUR][1000 genomes]
rs7648514	0.91[EUR][1000 genomes]
rs7652131	0.84[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs9311485	0.92[EUR][1000 genomes]
rs9682464	0.82[AMR][1000 genomes]
rs9812543	0.93[EUR][1000 genomes]
rs9813024	0.88[EUR][1000 genomes]
rs9831409	0.93[EUR][1000 genomes]
rs9836178	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9839035	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9842974	0.92[EUR][1000 genomes]
rs9844736	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9846976	0.92[EUR][1000 genomes]
rs9865094	0.92[EUR][1000 genomes]
rs9870898	0.81[EUR][1000 genomes]
rs9876403	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9985365	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9847024	MUSTN1	cis	Artery Aorta	GTEx
rs9847024	ITIH4-AS1	cis	lung	GTEx
rs9847024	ITIH4-AS1	cis	Artery Tibial	GTEx
rs9847024	ITIH4-AS1	cis	Artery Aorta	GTEx

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52931800-52965400	Weak transcription	Spleen	Spleen
2	chr3:52932000-52964000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:52932000-52970000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:52932000-52978000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:52932200-52961400	Weak transcription	HSMMtube	muscle
6	chr3:52932200-52961800	Weak transcription	A549	lung
7	chr3:52932200-52963000	Weak transcription	Stomach Mucosa	stomach
8	chr3:52932200-52966400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:52932200-52967800	Weak transcription	HSMM	muscle
10	chr3:52932200-52968600	Weak transcription	Osteobl	bone
11	chr3:52932200-52968800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:52932200-52968800	Weak transcription	Fetal Brain Male	brain
13	chr3:52932400-52968600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:52932400-52968600	Weak transcription	NHDF-Ad	bronchial
15	chr3:52932400-52968800	Weak transcription	NHEK	skin
16	chr3:52935600-52968600	Strong transcription	Dnd41	blood
17	chr3:52937200-52959800	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr3:52939600-52961200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr3:52941800-52961600	Weak transcription	Colonic Mucosa	Colon
20	chr3:52941800-52980200	Weak transcription	Psoas Muscle	Psoas
21	chr3:52943600-52962400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:52943600-52964000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:52945200-52960000	Weak transcription	Gastric	stomach
24	chr3:52947400-52968000	Weak transcription	Fetal Lung	lung
25	chr3:52947600-52960800	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr3:52947600-52963000	Weak transcription	Fetal Heart	heart
27	chr3:52949000-52962400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr3:52949000-52968800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:52949200-52962800	Weak transcription	K562	blood
30	chr3:52950000-52966600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr3:52951200-52966400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:52951400-52964400	Strong transcription	Fetal Intestine Large	intestine
33	chr3:52952000-52968600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr3:52952800-52965600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr3:52953000-52963000	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr3:52953400-52961400	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr3:52953400-52961400	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr3:52953800-52964600	Weak transcription	Fetal Kidney	kidney
39	chr3:52954000-52960000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr3:52954000-52962000	Weak transcription	HMEC	breast
41	chr3:52954000-52964000	Weak transcription	Rectal Smooth Muscle	rectum
42	chr3:52954000-53012200	Weak transcription	Esophagus	oesophagus
43	chr3:52954200-52961600	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr3:52954200-52961800	Weak transcription	Brain Angular Gyrus	brain
45	chr3:52954200-52961800	Weak transcription	Right Ventricle	heart
46	chr3:52954200-53012200	Weak transcription	Pancreas	Pancrea
47	chr3:52954400-52959600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr3:52954400-52960000	Weak transcription	Lung	lung
49	chr3:52954400-52963600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr3:52954400-52964800	Weak transcription	Ovary	ovary

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