Variant report

Variant	rs12498904
Chromosome Location	chr4:95454259-95454260
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:95372094..95374862-chr4:95453134..95454857,2	K562	blood:
2	chr4:95453797..95455503-chr4:95458519..95460892,2	K562	blood:
3	chr4:95373570..95375959-chr4:95453474..95457865,4	K562	blood:
4	chr4:95377886..95380417-chr4:95453413..95456083,2	K562	blood:
5	chr4:95452128..95455123-chr4:95466156..95467700,2	K562	blood:

Variant related genes	Relation type
ENSG00000163110	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10025074	0.87[ASN][1000 genomes]
rs10213504	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11726587	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11731606	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]
rs2452581	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2510766	0.87[ASN][1000 genomes]
rs2510771	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs3805274	0.87[ASN][1000 genomes]
rs3805283	0.87[ASN][1000 genomes]
rs3805286	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805288	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3828523	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6830074	0.87[ASN][1000 genomes]
rs7683990	0.93[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
rs12498904	PDLIM5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:84 , 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	chr4:95438200-95454600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr4:95438400-95454800	Weak transcription	Hela-S3	cervix
6	chr4:95440400-95455000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr4:95440600-95454600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr4:95440600-95454800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr4:95440600-95456200	Weak transcription	Spleen	Spleen
10	chr4:95440600-95456400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:95440600-95456600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr4:95441400-95455000	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr4:95441600-95454600	Weak transcription	Primary B cells from peripheral blood	blood
14	chr4:95442000-95469600	Weak transcription	Primary T cells from cord blood	blood
15	chr4:95442600-95455200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr4:95445000-95454600	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr4:95445000-95454800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr4:95447400-95455000	Weak transcription	HepG2	liver
19	chr4:95447800-95457200	Weak transcription	NHLF	lung
20	chr4:95448600-95456200	Weak transcription	Brain Substantia Nigra	brain
21	chr4:95448600-95456600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr4:95449000-95454600	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr4:95449000-95456000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:95449200-95454600	Weak transcription	HSMM	muscle
25	chr4:95449200-95455800	Weak transcription	HSMMtube	muscle
26	chr4:95449200-95470200	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr4:95449400-95455600	Weak transcription	Fetal Muscle Leg	muscle
28	chr4:95449400-95456200	Weak transcription	Ovary	ovary
29	chr4:95449400-95457200	Enhancers	Fetal Heart	heart
30	chr4:95449600-95455000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr4:95449800-95460400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr4:95450200-95454600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr4:95450200-95454600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr4:95450200-95456400	Enhancers	Osteobl	bone
35	chr4:95450400-95454800	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr4:95450400-95454800	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr4:95450400-95454800	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr4:95450400-95455800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr4:95450400-95455800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr4:95450400-95456000	Weak transcription	Aorta	Aorta
41	chr4:95450400-95456000	Weak transcription	Pancreas	Pancrea
42	chr4:95450400-95456200	Weak transcription	Stomach Smooth Muscle	stomach
43	chr4:95450400-95456400	Weak transcription	Right Ventricle	heart
44	chr4:95450400-95465800	Weak transcription	Lung	lung
45	chr4:95450600-95459600	Weak transcription	Brain Angular Gyrus	brain
46	chr4:95451200-95455400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr4:95451200-95456000	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr4:95451400-95454600	Weak transcription	Colon Smooth Muscle	Colon
49	chr4:95451600-95454600	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr4:95451600-95455000	Weak transcription	Adipose Nuclei	Adipose

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