Variant report

Variant	rs6858843
Chromosome Location	chr4:20739530-20739531
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	chr4:20733613..20735469-chr4:20737753..20739786,2	K562	blood:
2	chr4:20736248..20737799-chr4:20738056..20739802,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10031524	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10938803	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11936560	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11940062	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1820505	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2114474	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2322687	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3764965	0.82[EUR][1000 genomes]
rs3816874	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4577580	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61428210	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6447971	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6447972	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6447973	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6811933	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6857386	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7663837	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7668797	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7688592	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7689421	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7694208	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs964019	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[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	nsv1010145	chr4:20601908-21057992	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv537052	chr4:20601908-21057992	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv1014941	chr4:20611726-21345226	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv537053	chr4:20611726-21345226	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv829876	chr4:20638736-20835621	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv869522	chr4:20724433-20938248	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6858843	C4orf28	Cis_1M	lymphoblastoid	RTeQTL
rs6858843	PACRGL	cis	lung	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:20703000-20741400	Weak transcription	Stomach Mucosa	stomach
2	chr4:20703200-20741000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr4:20724400-20740000	Weak transcription	GM12878-XiMat	blood
4	chr4:20724600-20742000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr4:20724800-20741600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr4:20725000-20740600	Weak transcription	Colon Smooth Muscle	Colon
7	chr4:20725000-20753000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr4:20725600-20740000	Weak transcription	Brain Anterior Caudate	brain
9	chr4:20726000-20740000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr4:20726200-20740400	Weak transcription	Colonic Mucosa	Colon
11	chr4:20730600-20739600	Weak transcription	HUVEC	blood vessel
12	chr4:20730600-20757600	Weak transcription	HSMM	muscle
13	chr4:20732600-20758400	Weak transcription	Brain Angular Gyrus	brain
14	chr4:20735200-20741600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
15	chr4:20736000-20747800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr4:20736200-20741600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
17	chr4:20736800-20741400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr4:20737000-20740600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
19	chr4:20737400-20741200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:20737400-20741400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
21	chr4:20737600-20740600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr4:20738000-20740800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr4:20738200-20740600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
24	chr4:20738200-20741200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr4:20738400-20740200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr4:20738400-20740200	ZNF genes & repeats	A549	lung
27	chr4:20738400-20740600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
28	chr4:20738400-20740800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr4:20738400-20740800	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
30	chr4:20738400-20740800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
31	chr4:20738400-20740800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr4:20738400-20740800	ZNF genes & repeats	Brain Germinal Matrix	brain
33	chr4:20738400-20740800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
34	chr4:20738400-20740800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
35	chr4:20738400-20740800	ZNF genes & repeats	Fetal Brain Female	brain
36	chr4:20738400-20740800	ZNF genes & repeats	Ovary	ovary
37	chr4:20738400-20741000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr4:20738400-20741000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
39	chr4:20738400-20741600	ZNF genes & repeats	Fetal Lung	lung
40	chr4:20738400-20741800	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr4:20738600-20739600	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
42	chr4:20738600-20739600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
43	chr4:20738600-20739600	ZNF genes & repeats	Fetal Brain Male	brain
44	chr4:20738600-20739600	Strong transcription	K562	blood
45	chr4:20738600-20739800	Strong transcription	Primary B cells from peripheral blood	blood
46	chr4:20738600-20740400	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
47	chr4:20738600-20740400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr4:20738600-20740600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr4:20738600-20740600	ZNF genes & repeats	Primary T cells from cord blood	blood
50	chr4:20738600-20740600	ZNF genes & repeats	Fetal Muscle Trunk	muscle

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