Variant report

Variant	rs4001305
Chromosome Location	chr4:120359236-120359237
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10017335	0.83[EUR][1000 genomes]
rs10017389	0.82[EUR][1000 genomes]
rs10019406	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10019522	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10020027	0.81[EUR][1000 genomes]
rs10026736	0.81[EUR][1000 genomes]
rs11934314	0.81[EUR][1000 genomes]
rs17008998	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17009122	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28394590	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28408407	0.80[EUR][1000 genomes]
rs28461559	0.80[EUR][1000 genomes]
rs28529639	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28567426	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28571712	0.81[EUR][1000 genomes]
rs28587175	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28626372	0.82[EUR][1000 genomes]
rs28655325	0.82[EUR][1000 genomes]
rs2892848	0.83[EUR][1000 genomes]
rs34004415	0.82[EUR][1000 genomes]
rs34147052	0.90[AMR][1000 genomes]
rs34378623	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34566984	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34792640	0.84[AMR][1000 genomes]
rs34954036	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34965784	0.91[AMR][1000 genomes]
rs35111011	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35494005	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66506550	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67265404	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71614422	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71614434	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs71614435	0.80[AMR][1000 genomes]
rs71614438	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs71614443	0.81[EUR][1000 genomes]
rs71614444	0.83[EUR][1000 genomes]
rs71629403	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs71629404	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72918584	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7659501	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7659551	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7664458	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7681978	0.82[EUR][1000 genomes]
rs9683609	0.83[AMR][1000 genomes]
rs9683709	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9684475	0.84[AMR][1000 genomes]
rs9685777	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9685784	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9759478	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9760442	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9994730	0.83[EUR][1000 genomes]
rs9994810	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012868	chr4:120014630-120464880	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv537232	chr4:120014630-120464880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv428769	chr4:120205572-120363323	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv879841	chr4:120244085-120388406	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv879842	chr4:120244085-120424087	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv427694	chr4:120250511-120501728	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	esv2538163	chr4:120252854-120388678	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv966315	chr4:120323446-120375667	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv879843	chr4:120326323-120502461	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv879844	chr4:120341296-120449810	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	nsv879846	chr4:120341296-120491714	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
13	nsv879845	chr4:120341296-120502461	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	nsv980303	chr4:120358380-120365634	Weak transcription Strong transcription Active TSS	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4001305	RP11-33B1.4	cis	Whole Blood	GTEx
rs4001305	RP11-33B1.1	cis	Nerve Tibial	GTEx
rs4001305	RP11-33B1.1	cis	Whole Blood	GTEx
rs4001305	FLJ14186///LOC284701///LOC441124///LOC728624	Cis_1M	lymphoblastoid	RTeQTL
rs4001305	RP11-33B1.1	cis	Heart Left Ventricle	GTEx
rs4001305	RP11-384K6.6	cis	Whole Blood	GTEx
rs4001305	RP11-33B1.1	cis	Esophagus Mucosa	GTEx
rs4001305	RP11-33B1.1	cis	lung	GTEx
rs4001305	LOC645513	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120326600-120360800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:120327200-120361400	Weak transcription	Fetal Intestine Small	intestine
3	chr4:120328800-120375200	Weak transcription	Ovary	ovary
4	chr4:120330200-120367600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr4:120330600-120365200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr4:120330600-120366400	Weak transcription	Fetal Stomach	stomach
7	chr4:120336800-120365400	Weak transcription	Fetal Intestine Large	intestine
8	chr4:120341800-120367800	Weak transcription	Adipose Nuclei	Adipose
9	chr4:120345400-120375200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr4:120349400-120375400	Weak transcription	Lung	lung
11	chr4:120353200-120375000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr4:120353200-120375200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr4:120353200-120375200	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr4:120353400-120375200	Weak transcription	Pancreas	Pancrea
15	chr4:120353800-120366000	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr4:120354000-120368000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr4:120354000-120375000	Weak transcription	Placenta	Placenta
18	chr4:120354400-120375200	Weak transcription	Fetal Muscle Trunk	muscle
19	chr4:120354600-120375200	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr4:120354800-120375600	Weak transcription	Spleen	Spleen
21	chr4:120355000-120375200	Weak transcription	Duodenum Mucosa	Duodenum
22	chr4:120355200-120375000	Weak transcription	Fetal Muscle Leg	muscle
23	chr4:120355400-120359800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr4:120355800-120369200	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr4:120355800-120375000	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr4:120356600-120363200	Weak transcription	Liver	Liver
27	chr4:120357800-120361400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr4:120357800-120375000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr4:120358200-120368600	Weak transcription	Brain Anterior Caudate	brain
30	chr4:120358400-120369600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr4:120358400-120374800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr4:120358600-120375200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr4:120358800-120375200	Weak transcription	Stomach Smooth Muscle	stomach
34	chr4:120359000-120375400	Weak transcription	Left Ventricle	heart

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