Variant report

Variant	rs1043862
Chromosome Location	chr4:95588823-95588824
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	chr4:95587418..95589202-chr4:95610203..95611805,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10010013	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10014050	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10025288	1.00[ASW][hapmap];0.94[CEU][hapmap];0.94[CHD][hapmap];0.95[LWK][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10025410	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10049504	0.83[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1056772	0.93[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];0.86[LWK][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11097431	0.81[CHD][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs11097432	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1134984	0.96[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs11550270	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12294	0.91[EUR][1000 genomes]
rs12331809	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12331835	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12331920	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1509617	0.89[CEU][hapmap];0.86[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs17021981	0.83[CEU][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17336353	0.81[CHD][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs1802345	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2452593	0.81[TSI][hapmap]
rs28376560	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28376694	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28479946	0.82[EUR][1000 genomes]
rs28654759	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28709926	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828518	0.81[CHD][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs6816687	0.81[CHD][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs6840428	0.83[CEU][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7285	0.93[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];0.88[LWK][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7655928	0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7656545	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[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
rs1043862	PDLIM5	cis	multi-tissue	Pritchard

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95525000-95590000	Weak transcription	Lung	lung
2	chr4:95527800-95592200	Weak transcription	Pancreas	Pancrea
3	chr4:95533800-95594200	Weak transcription	Gastric	stomach
4	chr4:95537600-95592800	Weak transcription	Fetal Stomach	stomach
5	chr4:95540200-95597800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr4:95541200-95595600	Weak transcription	Primary T cells from cord blood	blood
7	chr4:95559000-95590200	Weak transcription	Right Ventricle	heart
8	chr4:95563600-95589000	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr4:95564000-95595000	Weak transcription	NHDF-Ad	bronchial
10	chr4:95570800-95599800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr4:95573600-95595000	Weak transcription	Small Intestine	intestine
12	chr4:95574800-95591600	Weak transcription	Stomach Mucosa	stomach
13	chr4:95575000-95590800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr4:95575800-95590200	Strong transcription	Osteobl	bone
15	chr4:95576200-95598000	Weak transcription	Aorta	Aorta
16	chr4:95576200-95598200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:95578600-95589200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr4:95578600-95593800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr4:95579000-95592400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr4:95580000-95597800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr4:95581400-95590000	Strong transcription	NH-A	brain
22	chr4:95582000-95595400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr4:95582000-95599800	Weak transcription	NHEK	skin
24	chr4:95582400-95592200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr4:95582400-95594200	Weak transcription	Esophagus	oesophagus
26	chr4:95582400-95596200	Weak transcription	Fetal Muscle Leg	muscle
27	chr4:95582400-95598200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr4:95582600-95589600	Strong transcription	Liver	Liver
29	chr4:95582600-95593800	Weak transcription	Ovary	ovary
30	chr4:95582600-95600000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr4:95582800-95598000	Weak transcription	Fetal Heart	heart
32	chr4:95585000-95592200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr4:95585200-95592200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr4:95585200-95592200	Weak transcription	Adipose Nuclei	Adipose
35	chr4:95585200-95593600	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr4:95585200-95598200	Weak transcription	Colon Smooth Muscle	Colon
37	chr4:95585800-95590400	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr4:95586000-95594000	Weak transcription	Duodenum Mucosa	Duodenum
39	chr4:95586000-95598000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr4:95586600-95594000	Weak transcription	Fetal Intestine Small	intestine
41	chr4:95586600-95594200	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr4:95587200-95589200	Strong transcription	HUVEC	blood vessel
43	chr4:95587200-95589800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr4:95587400-95590200	Strong transcription	HMEC	breast
45	chr4:95587400-95598000	Weak transcription	HSMMtube	muscle
46	chr4:95587600-95589600	Weak transcription	NHLF	lung
47	chr4:95587600-95590000	Weak transcription	Fetal Kidney	kidney
48	chr4:95587600-95590200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr4:95587600-95590800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr4:95587600-95591000	Weak transcription	Muscle Satellite Cultured Cells	--

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