Variant report

Variant	rs13144541
Chromosome Location	chr4:79246209-79246210
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1017649	0.82[GIH][hapmap];0.83[MEX][hapmap];0.82[YRI][hapmap]
rs12505633	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12505887	0.87[EUR][1000 genomes]
rs12511889	0.82[EUR][1000 genomes]
rs12641094	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13117388	0.81[GIH][hapmap];0.87[MEX][hapmap]
rs13119684	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17455826	0.81[GIH][hapmap];0.87[MEX][hapmap]
rs345513	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs345515	0.89[CEU][hapmap]
rs34643532	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs41537644	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4515188	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7661907	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7693120	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534024	chr4:78785189-79437403	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv525530	chr4:79024524-79266563	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv1010782	chr4:79057839-79387207	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv829978	chr4:79144453-79291868	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv3332661	chr4:79246075-79246466	Weak transcription Enhancers Strong transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13144541	PARM1	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79220400-79246600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr4:79220400-79246600	Weak transcription	HMEC	breast
3	chr4:79221200-79263000	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr4:79229800-79257600	Weak transcription	Fetal Stomach	stomach
5	chr4:79230200-79268600	Weak transcription	Pancreas	Pancrea
6	chr4:79230600-79258000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:79231600-79260400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:79235800-79246600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr4:79236000-79249200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr4:79237800-79252800	Weak transcription	Fetal Kidney	kidney
11	chr4:79238000-79263200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr4:79238600-79246600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr4:79240400-79246600	Weak transcription	Fetal Heart	heart
14	chr4:79240400-79263000	Weak transcription	Psoas Muscle	Psoas
15	chr4:79240600-79252400	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr4:79241200-79250200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr4:79241400-79252600	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr4:79241600-79246600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr4:79241600-79252400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr4:79241600-79252400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr4:79241600-79257600	Weak transcription	Left Ventricle	heart
22	chr4:79241800-79246600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr4:79241800-79256400	Weak transcription	HepG2	liver
24	chr4:79243800-79247800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr4:79245000-79250600	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr4:79245000-79252400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr4:79245000-79252800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr4:79245400-79249200	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr4:79246000-79247000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr4:79246200-79247000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr4:79246200-79247200	Enhancers	NHDF-Ad	bronchial
32	chr4:79246200-79247400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr4:79246200-79247400	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr4:79246200-79247400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr4:79246200-79247600	Enhancers	Fetal Intestine Large	intestine
36	chr4:79246200-79248000	Enhancers	Fetal Intestine Small	intestine

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