Variant report

Variant	rs7681843
Chromosome Location	chr4:95595308-95595309
allele	A/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	chr4:95595059-95597064	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr4:95595039-95595775	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr4:95595256-95595574	K562	blood:	n/a	n/a
4	POLR2A	chr4:95594940-95595785	A549	lung:	n/a	n/a

Variant related genes	Relation type
ENSG00000249951	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10015716	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs1043848	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10590	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12500116	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12505788	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12510147	0.81[CEU][hapmap]
rs12511169	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs13121500	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1493112	0.81[CEU][hapmap]
rs17021918	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17021972	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2136486	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs2280003	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2452597	0.84[CEU][hapmap]
rs2452598	0.81[CEU][hapmap]
rs2452600	0.84[CEU][hapmap]
rs2510767	0.81[CEU][hapmap]
rs35964087	0.85[EUR][1000 genomes]
rs3762876	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4699316	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61597100	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6817664	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6822544	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6837308	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7659399	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7674144	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7694162	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs998071	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][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
rs7681843	PDLIM5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:35 , 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	chr4:95570800-95599800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr4:95576200-95598000	Weak transcription	Aorta	Aorta
5	chr4:95576200-95598200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:95580000-95597800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr4:95582000-95595400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr4:95582000-95599800	Weak transcription	NHEK	skin
9	chr4:95582400-95596200	Weak transcription	Fetal Muscle Leg	muscle
10	chr4:95582400-95598200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr4:95582600-95600000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr4:95582800-95598000	Weak transcription	Fetal Heart	heart
13	chr4:95585200-95598200	Weak transcription	Colon Smooth Muscle	Colon
14	chr4:95586000-95598000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:95587400-95598000	Weak transcription	HSMMtube	muscle
16	chr4:95587800-95598400	Weak transcription	HSMM	muscle
17	chr4:95588000-95598400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr4:95588000-95599800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr4:95589800-95597600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr4:95589800-95598000	Weak transcription	Stomach Smooth Muscle	stomach
21	chr4:95590000-95599800	Weak transcription	NH-A	brain
22	chr4:95590200-95599800	Weak transcription	HMEC	breast
23	chr4:95590800-95601200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr4:95591600-95597800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr4:95591800-95597800	Weak transcription	Osteobl	bone
26	chr4:95592200-95595600	Weak transcription	HUVEC	blood vessel
27	chr4:95592400-95598200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr4:95592600-95598000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr4:95592600-95601200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr4:95592800-95597800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr4:95592800-95599800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr4:95593000-95597400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr4:95594200-95598200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr4:95594600-95595400	Weak transcription	Fetal Kidney	kidney
35	chr4:95595200-95596000	Weak transcription	A549	lung

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