Variant report

Variant	rs17021981
Chromosome Location	chr4:95594456-95594457
allele	C/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	POLR2A	chr4:95594309-95594832	HepG2	liver:	n/a	n/a
2	POLR2A	chr4:95593243-95594521	K562	blood:	n/a	n/a
3	POLR2A	chr4:95593489-95594506	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr4:95594185-95594925	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr4:95593530-95594634	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:95592542..95594802-chr4:95595610..95598879,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249951	TF binding region
ENSG00000249951	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10010013	0.88[AMR][1000 genomes]
rs10014050	0.88[AMR][1000 genomes]
rs10025288	0.87[CEU][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10025410	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10049504	1.00[CEU][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1043862	0.83[CEU][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1056772	0.87[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11097432	0.87[CEU][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1134984	0.83[EUR][1000 genomes]
rs11550270	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12294	0.81[EUR][1000 genomes]
rs12331809	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12331835	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12331920	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1509617	0.83[EUR][1000 genomes]
rs1802345	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28376560	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28376694	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28479946	0.92[EUR][1000 genomes]
rs28654759	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28709926	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6840428	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7285	0.87[CEU][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7655928	0.88[AMR][1000 genomes]
rs7656545	0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932216	chr4:95501261-96109807	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1003860	chr4:95507683-96120619	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv869528	chr4:95537649-96368018	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1005816	chr4:95573444-95902704	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17021981	PDLIM5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95540200-95597800	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr4:95541200-95595600	Weak transcription	Primary T cells from cord blood	blood
3	chr4:95564000-95595000	Weak transcription	NHDF-Ad	bronchial
4	chr4:95570800-95599800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr4:95573600-95595000	Weak transcription	Small Intestine	intestine
6	chr4:95576200-95598000	Weak transcription	Aorta	Aorta
7	chr4:95576200-95598200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:95580000-95597800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr4:95582000-95595400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr4:95582000-95599800	Weak transcription	NHEK	skin
11	chr4:95582400-95596200	Weak transcription	Fetal Muscle Leg	muscle
12	chr4:95582400-95598200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr4:95582600-95600000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr4:95582800-95598000	Weak transcription	Fetal Heart	heart
15	chr4:95585200-95598200	Weak transcription	Colon Smooth Muscle	Colon
16	chr4:95586000-95598000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:95587400-95598000	Weak transcription	HSMMtube	muscle
18	chr4:95587800-95598400	Weak transcription	HSMM	muscle
19	chr4:95588000-95598400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr4:95588000-95599800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr4:95588200-95595200	Weak transcription	Placenta	Placenta
22	chr4:95589800-95597600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr4:95589800-95598000	Weak transcription	Stomach Smooth Muscle	stomach
24	chr4:95590000-95599800	Weak transcription	NH-A	brain
25	chr4:95590200-95599800	Weak transcription	HMEC	breast
26	chr4:95590800-95601200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr4:95591600-95597800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr4:95591800-95597800	Weak transcription	Osteobl	bone
29	chr4:95592200-95595600	Weak transcription	HUVEC	blood vessel
30	chr4:95592400-95598200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr4:95592600-95595200	Enhancers	A549	lung
32	chr4:95592600-95598000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr4:95592600-95601200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr4:95592800-95597800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr4:95592800-95599800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr4:95593000-95594800	Weak transcription	Adipose Nuclei	Adipose
37	chr4:95593000-95597400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr4:95593800-95594600	Enhancers	Fetal Kidney	kidney
39	chr4:95594200-95598200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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