Variant report

Variant	rs3805286
Chromosome Location	chr4:95455600-95455601
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:95455418..95457640-chr4:95458337..95460219,4	K562	blood:
2	chr4:95404882..95407708-chr4:95454593..95456419,2	K562	blood:
3	chr4:95373570..95375959-chr4:95453474..95457865,4	K562	blood:
4	chr4:95377886..95380417-chr4:95453413..95456083,2	K562	blood:
5	chr4:95455231..95457643-chr4:95461903..95464194,2	K562	blood:
6	chr4:95449221..95452678-chr4:95455541..95457733,4	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10025074	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs10213504	1.00[CHB][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs11726587	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11731606	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12498904	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12502803	0.84[ASN][1000 genomes]
rs17336353	0.82[CHB][hapmap]
rs2162346	0.96[YRI][hapmap]
rs2452581	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2452593	1.00[CHB][hapmap]
rs2452594	0.82[CHB][hapmap]
rs2510766	0.87[ASN][1000 genomes]
rs2510771	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs3792664	0.85[CEU][hapmap]
rs3805274	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs3805283	0.83[CEU][hapmap];1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs3805288	0.86[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3828518	0.82[CHB][hapmap]
rs3828523	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6816687	0.82[CHB][hapmap]
rs6830074	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs7656545	0.82[CHB][hapmap]
rs7679284	0.82[CHB][hapmap];0.83[JPT][hapmap];0.85[MEX][hapmap]
rs7683990	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9307144	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993495	chr4:94992315-95482578	Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv594901	chr4:95254730-95493246	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1003743	chr4:95255957-95469831	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3805286	PDLIM5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95422400-95482800	Weak transcription	Fetal Muscle Trunk	muscle
2	chr4:95430000-95456200	Weak transcription	Small Intestine	intestine
3	chr4:95437600-95456000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr4:95440600-95456200	Weak transcription	Spleen	Spleen
5	chr4:95440600-95456400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:95440600-95456600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr4:95442000-95469600	Weak transcription	Primary T cells from cord blood	blood
8	chr4:95447800-95457200	Weak transcription	NHLF	lung
9	chr4:95448600-95456200	Weak transcription	Brain Substantia Nigra	brain
10	chr4:95448600-95456600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr4:95449000-95456000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:95449200-95455800	Weak transcription	HSMMtube	muscle
13	chr4:95449200-95470200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr4:95449400-95455600	Weak transcription	Fetal Muscle Leg	muscle
15	chr4:95449400-95456200	Weak transcription	Ovary	ovary
16	chr4:95449400-95457200	Enhancers	Fetal Heart	heart
17	chr4:95449800-95460400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr4:95450200-95456400	Enhancers	Osteobl	bone
19	chr4:95450400-95455800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr4:95450400-95455800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr4:95450400-95456000	Weak transcription	Aorta	Aorta
22	chr4:95450400-95456000	Weak transcription	Pancreas	Pancrea
23	chr4:95450400-95456200	Weak transcription	Stomach Smooth Muscle	stomach
24	chr4:95450400-95456400	Weak transcription	Right Ventricle	heart
25	chr4:95450400-95465800	Weak transcription	Lung	lung
26	chr4:95450600-95459600	Weak transcription	Brain Angular Gyrus	brain
27	chr4:95451200-95456000	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr4:95452000-95456600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr4:95452400-95457600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr4:95452600-95456600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr4:95452600-95458000	Enhancers	HUVEC	blood vessel
32	chr4:95453400-95456800	Enhancers	HMEC	breast
33	chr4:95453800-95455600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr4:95453800-95459400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr4:95453800-95459600	Weak transcription	NHDF-Ad	bronchial
36	chr4:95453800-95460400	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr4:95453800-95465400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr4:95454000-95455800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr4:95454000-95456000	Weak transcription	NH-A	brain
40	chr4:95454000-95457000	Enhancers	Stomach Mucosa	stomach
41	chr4:95454000-95457200	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr4:95454200-95456000	Weak transcription	Esophagus	oesophagus
43	chr4:95454200-95456200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr4:95454200-95456400	Weak transcription	Left Ventricle	heart
45	chr4:95454200-95457000	Enhancers	Duodenum Mucosa	Duodenum
46	chr4:95454200-95458400	Enhancers	Fetal Intestine Large	intestine
47	chr4:95454400-95457000	Flanking Active TSS	K562	blood
48	chr4:95454400-95458200	Enhancers	Fetal Intestine Small	intestine
49	chr4:95454400-95458400	Enhancers	Placenta Amnion	Placenta Amnion
50	chr4:95454400-95459000	Enhancers	ES-I3 Cell Line	embryonic stem cell

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