Variant report

Variant	rs3805283
Chromosome Location	chr4:95458074-95458075
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:95456523..95459012-chr4:95469903..95471763,2	MCF-7	breast:
2	chr4:95457924..95459634-chr4:95461855..95464045,2	K562	blood:
3	chr4:95455791..95459041-chr4:95471671..95474537,3	K562	blood:
4	chr4:95371767..95374402-chr4:95456594..95458553,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000203436	Chromatin interaction
ENSG00000163110	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10000208	0.91[EUR][1000 genomes]
rs10025074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10213504	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11726587	0.91[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11731606	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs12498904	0.87[ASN][1000 genomes]
rs17336353	0.82[CHB][hapmap]
rs2452581	1.00[ASN][1000 genomes]
rs2452593	1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs2452594	0.82[CHB][hapmap]
rs2510766	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2510771	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28416638	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3792664	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs3805271	0.89[ASN][1000 genomes]
rs3805272	0.89[ASN][1000 genomes]
rs3805274	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805286	0.83[CEU][hapmap];1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs3805288	0.83[CEU][hapmap]
rs3828518	0.82[CHB][hapmap]
rs6812098	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs6816687	0.82[CHB][hapmap]
rs6830074	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7656545	0.82[CHB][hapmap]
rs7679284	0.82[CHB][hapmap]
rs7683990	0.87[ASN][1000 genomes]
rs9307144	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[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
rs3805283	PDLIM5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 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	chr4:95442000-95469600	Weak transcription	Primary T cells from cord blood	blood
3	chr4:95449200-95470200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr4:95449800-95460400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr4:95450400-95465800	Weak transcription	Lung	lung
6	chr4:95450600-95459600	Weak transcription	Brain Angular Gyrus	brain
7	chr4:95453800-95459400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr4:95453800-95459600	Weak transcription	NHDF-Ad	bronchial
9	chr4:95453800-95460400	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr4:95453800-95465400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr4:95454200-95458400	Enhancers	Fetal Intestine Large	intestine
12	chr4:95454400-95458200	Enhancers	Fetal Intestine Small	intestine
13	chr4:95454400-95458400	Enhancers	Placenta Amnion	Placenta Amnion
14	chr4:95454400-95459000	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr4:95454600-95458400	Enhancers	Liver	Liver
16	chr4:95454600-95458400	Enhancers	Rectal Smooth Muscle	rectum
17	chr4:95454600-95460200	Enhancers	Colon Smooth Muscle	Colon
18	chr4:95454600-95462600	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr4:95454800-95458200	Enhancers	Placenta	Placenta
20	chr4:95455000-95459000	Enhancers	Adipose Nuclei	Adipose
21	chr4:95455400-95458800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr4:95455600-95460000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr4:95455800-95460200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr4:95456000-95459600	Enhancers	H1 Cell Line	embryonic stem cell
25	chr4:95456200-95458200	Enhancers	Stomach Smooth Muscle	stomach
26	chr4:95456200-95463200	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr4:95456400-95459600	Enhancers	A549	lung
28	chr4:95456400-95460600	Weak transcription	NHEK	skin
29	chr4:95456400-95462800	Enhancers	HSMMtube	muscle
30	chr4:95456600-95458400	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr4:95456600-95459800	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr4:95456600-95460200	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr4:95456600-95460800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr4:95456800-95458200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr4:95456800-95460800	Weak transcription	HMEC	breast
36	chr4:95456800-95465000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr4:95456800-95469800	Weak transcription	Ovary	ovary
38	chr4:95456800-95470200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr4:95457000-95459600	Enhancers	HSMM	muscle
40	chr4:95457000-95469800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr4:95457200-95458200	Enhancers	NHLF	lung
42	chr4:95457200-95458400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
43	chr4:95457200-95458400	Enhancers	Muscle Satellite Cultured Cells	--
44	chr4:95457200-95458400	Enhancers	Fetal Kidney	kidney
45	chr4:95457200-95459600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr4:95457200-95459800	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr4:95457200-95460000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr4:95457400-95458200	Weak transcription	Brain Anterior Caudate	brain
49	chr4:95457400-95458200	Enhancers	Duodenum Mucosa	Duodenum
50	chr4:95457400-95458400	Enhancers	GM12878-XiMat	blood

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