Variant report

Variant	rs17379209
Chromosome Location	chr4:95411302-95411303
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:95410422..95412856-chr4:95417463..95420295,3	K562	blood:
2	chr4:95410894..95412741-chr4:95425809..95427344,2	K562	blood:
3	chr4:95372926..95375393-chr4:95409110..95411441,2	MCF-7	breast:
4	chr4:95406401..95409166-chr4:95410541..95413681,3	K562	blood:

Variant related genes	Relation type
ENSG00000163110	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1082514	0.94[ASN][1000 genomes]
rs17378658	0.87[CEU][hapmap];0.89[EUR][1000 genomes]
rs2555216	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2639793	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2639795	0.80[CEU][hapmap];0.82[EUR][1000 genomes]
rs28502775	0.89[EUR][1000 genomes]
rs35793531	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3805301	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5002911	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs699861	0.87[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73833924	0.94[ASN][1000 genomes]
rs774983	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs774988	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs774989	1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs774993	0.87[EUR][1000 genomes];0.94[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
rs17379209	PDLIM5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95375000-95440200	Weak transcription	Primary T cells from cord blood	blood
2	chr4:95387400-95420800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:95394400-95419200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr4:95394400-95428000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr4:95396600-95419000	Weak transcription	Duodenum Mucosa	Duodenum
6	chr4:95398400-95428400	Weak transcription	Small Intestine	intestine
7	chr4:95400400-95415200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr4:95400800-95440000	Weak transcription	Lung	lung
9	chr4:95401800-95420800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:95402000-95416800	Weak transcription	Pancreas	Pancrea
11	chr4:95402200-95412000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr4:95402200-95412200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr4:95402200-95412200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr4:95403000-95416600	Weak transcription	Left Ventricle	heart
15	chr4:95403800-95417800	Weak transcription	HepG2	liver
16	chr4:95404000-95415000	Weak transcription	Fetal Intestine Small	intestine
17	chr4:95404400-95412200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr4:95405000-95429000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr4:95406000-95419800	Weak transcription	GM12878-XiMat	blood
20	chr4:95406400-95411800	Weak transcription	HSMM	muscle
21	chr4:95407200-95428000	Weak transcription	Placenta	Placenta
22	chr4:95408000-95412200	Weak transcription	Right Ventricle	heart
23	chr4:95408000-95412600	Weak transcription	Stomach Mucosa	stomach
24	chr4:95408000-95428000	Weak transcription	K562	blood
25	chr4:95408200-95422000	Weak transcription	Fetal Muscle Trunk	muscle
26	chr4:95409000-95412200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr4:95409000-95422000	Weak transcription	Ovary	ovary
28	chr4:95409200-95411600	Weak transcription	Liver	Liver
29	chr4:95409400-95412200	Enhancers	HUVEC	blood vessel
30	chr4:95409400-95419000	Weak transcription	Aorta	Aorta
31	chr4:95409800-95412200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr4:95409800-95412200	Enhancers	Osteobl	bone
33	chr4:95410000-95412200	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr4:95410000-95412400	Enhancers	NHLF	lung
35	chr4:95410000-95412600	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr4:95410000-95412600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr4:95410200-95412600	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr4:95410200-95415000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr4:95410200-95415000	Weak transcription	Fetal Muscle Leg	muscle
40	chr4:95410200-95416000	Weak transcription	Fetal Intestine Large	intestine
41	chr4:95410200-95422000	Weak transcription	Right Atrium	heart
42	chr4:95410400-95411600	Weak transcription	NH-A	brain
43	chr4:95410400-95411800	Weak transcription	Colon Smooth Muscle	Colon
44	chr4:95410400-95415200	Weak transcription	Psoas Muscle	Psoas
45	chr4:95410600-95411600	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr4:95410600-95411600	Weak transcription	A549	lung
47	chr4:95410600-95411800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr4:95410600-95411800	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr4:95410600-95412000	Weak transcription	Fetal Heart	heart
50	chr4:95410600-95412000	Weak transcription	Hela-S3	cervix

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