Variant report

Variant	rs3805301
Chromosome Location	chr4:95412692-95412693
allele	C/T
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	chr4:95406401..95409166-chr4:95410541..95413681,3	K562	blood:

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1082514	0.94[ASN][1000 genomes]
rs17378658	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs17378777	0.87[YRI][hapmap]
rs17379209	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]
rs2433320	0.87[YRI][hapmap]
rs2433322	0.87[YRI][hapmap]
rs2438146	0.83[YRI][hapmap]
rs2510763	0.80[YRI][hapmap]
rs2555216	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2639793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2639795	0.81[CEU][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs28502775	0.89[EUR][1000 genomes]
rs35793531	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5002911	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs699861	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73833924	0.94[ASN][1000 genomes]
rs774983	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs774988	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs774989	1.00[JPT][hapmap];0.83[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
rs3805301	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	chr4:95403000-95416600	Weak transcription	Left Ventricle	heart
12	chr4:95403800-95417800	Weak transcription	HepG2	liver
13	chr4:95404000-95415000	Weak transcription	Fetal Intestine Small	intestine
14	chr4:95405000-95429000	Weak transcription	Primary hematopoietic stem cells	blood
15	chr4:95406000-95419800	Weak transcription	GM12878-XiMat	blood
16	chr4:95407200-95428000	Weak transcription	Placenta	Placenta
17	chr4:95408000-95428000	Weak transcription	K562	blood
18	chr4:95408200-95422000	Weak transcription	Fetal Muscle Trunk	muscle
19	chr4:95409000-95422000	Weak transcription	Ovary	ovary
20	chr4:95409400-95419000	Weak transcription	Aorta	Aorta
21	chr4:95410200-95415000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr4:95410200-95415000	Weak transcription	Fetal Muscle Leg	muscle
23	chr4:95410200-95416000	Weak transcription	Fetal Intestine Large	intestine
24	chr4:95410200-95422000	Weak transcription	Right Atrium	heart
25	chr4:95410400-95415200	Weak transcription	Psoas Muscle	Psoas
26	chr4:95410600-95413600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr4:95410600-95413600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr4:95410600-95415200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr4:95411000-95427800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr4:95411600-95413200	Enhancers	A549	lung
31	chr4:95411600-95413600	Enhancers	Muscle Satellite Cultured Cells	--
32	chr4:95411800-95413200	Enhancers	Pancreatic Islets	Pancreatic Islet
33	chr4:95411800-95413400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr4:95411800-95413400	Enhancers	HSMM	muscle
35	chr4:95411800-95413800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr4:95412000-95412800	Enhancers	NHDF-Ad	bronchial
37	chr4:95412000-95413200	Enhancers	Hela-S3	cervix
38	chr4:95412000-95413800	Enhancers	Fetal Heart	heart
39	chr4:95412200-95412800	Enhancers	Brain Anterior Caudate	brain
40	chr4:95412200-95412800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr4:95412200-95413000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr4:95412200-95413000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr4:95412200-95413200	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr4:95412200-95413200	Flanking Active TSS	NHEK	skin
45	chr4:95412200-95413600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr4:95412200-95413800	Enhancers	HMEC	breast
47	chr4:95412200-95416200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr4:95412400-95412800	Enhancers	Rectal Smooth Muscle	rectum
49	chr4:95412400-95413000	Flanking Active TSS	NHLF	lung
50	chr4:95412400-95413400	Enhancers	HSMMtube	muscle

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