Variant report

Variant	rs4942860
Chromosome Location	chr13:50198398-50198399
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	chr13:50016671..50019335-chr13:50197753..50200555,2	K562	blood:

Variant related genes	Relation type
ENSG00000102547	Chromatin interaction
ENSG00000136169	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1359541	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1359543	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1409015	0.81[ASN][1000 genomes]
rs2094108	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2146144	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2146146	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3969	0.82[EUR][1000 genomes]
rs4315259	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4409984	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4638463	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4942851	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4942854	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4942859	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7329454	0.83[ASN][1000 genomes]
rs7334387	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7981043	0.88[EUR][1000 genomes]
rs7994201	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs8000680	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9316462	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9316463	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9526580	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535268	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535270	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9535271	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535275	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9568284	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9568285	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9568286	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047311	chr13:49895019-50224227	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv916093	chr13:50050919-50290245	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers 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	29 gene(s)	inside rSNPs	diseases
3	nsv1054965	chr13:50102730-50251347	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv541771	chr13:50102730-50251347	Enhancers Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv900071	chr13:50107289-50286218	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv1043697	chr13:50129199-50249241	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	esv2752657	chr13:50144995-50244150	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4942860	ARL11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50191200-50199400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr13:50194600-50202000	Weak transcription	Esophagus	oesophagus
3	chr13:50194800-50198800	Weak transcription	Lung	lung
4	chr13:50194800-50198800	Weak transcription	Spleen	Spleen
5	chr13:50194800-50199200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr13:50194800-50199200	Weak transcription	Duodenum Mucosa	Duodenum
7	chr13:50194800-50199600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr13:50194800-50199600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr13:50194800-50199600	Weak transcription	Gastric	stomach
10	chr13:50194800-50199600	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr13:50194800-50200000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr13:50194800-50201800	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr13:50194800-50202000	Weak transcription	Primary B cells from cord blood	blood
14	chr13:50194800-50202000	Weak transcription	Primary hematopoietic stem cells	blood
15	chr13:50194800-50202000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr13:50194800-50202000	Weak transcription	Fetal Thymus	thymus
17	chr13:50194800-50202000	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr13:50194800-50202200	Weak transcription	Colonic Mucosa	Colon
19	chr13:50194800-50202200	Weak transcription	K562	blood
20	chr13:50195800-50199200	Enhancers	HepG2	liver
21	chr13:50195800-50200400	Enhancers	Fetal Heart	heart
22	chr13:50196200-50198600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr13:50196600-50199200	Weak transcription	Right Ventricle	heart
24	chr13:50196800-50199600	Weak transcription	Left Ventricle	heart
25	chr13:50196800-50199600	Weak transcription	Right Atrium	heart
26	chr13:50197000-50199400	Weak transcription	Adipose Nuclei	Adipose
27	chr13:50197000-50199600	Weak transcription	Fetal Lung	lung
28	chr13:50197000-50199600	Weak transcription	Ovary	ovary
29	chr13:50197000-50201800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr13:50198200-50199000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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