Variant report

Variant	rs4246821
Chromosome Location	chr5:178144495-178144496
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1000057	0.85[ASN][1000 genomes]
rs10042073	0.85[ASN][1000 genomes]
rs10072060	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12518753	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13188788	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1984703	0.85[ASN][1000 genomes]
rs2078257	0.85[ASN][1000 genomes]
rs3927097	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6898275	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7704813	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7711731	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7715476	0.85[ASN][1000 genomes]
rs7736628	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs931056	0.85[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	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1031666	chr5:177988601-178236068	Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv883217	chr5:178099758-178193081	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4246821	PDLIM7	cis	cerebellum	SCAN
rs4246821	ZNF354B	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178130000-178150600	ZNF genes & repeats	Adipose Nuclei	Adipose
2	chr5:178135400-178150600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr5:178135800-178147600	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
4	chr5:178135800-178155600	ZNF genes & repeats	Liver	Liver
5	chr5:178136200-178155200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
6	chr5:178136800-178150400	ZNF genes & repeats	Brain Substantia Nigra	brain
7	chr5:178136800-178150600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr5:178136800-178152800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
9	chr5:178137000-178149800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
10	chr5:178137000-178150600	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
11	chr5:178137000-178150600	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
12	chr5:178137200-178151000	ZNF genes & repeats	Fetal Brain Female	brain
13	chr5:178137400-178147800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr5:178137400-178150600	ZNF genes & repeats	Psoas Muscle	Psoas
15	chr5:178138400-178146000	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
16	chr5:178138400-178149800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr5:178138400-178155600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr5:178138600-178145400	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
19	chr5:178138600-178146600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
20	chr5:178138600-178147600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
21	chr5:178138600-178147600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
22	chr5:178138600-178147600	ZNF genes & repeats	Osteobl	bone
23	chr5:178138600-178148000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
24	chr5:178138600-178148800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
25	chr5:178138600-178149400	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
26	chr5:178138600-178149600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
27	chr5:178138600-178150400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr5:178138600-178150600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:178138600-178150600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr5:178138600-178150600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr5:178138800-178146600	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr5:178138800-178150200	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr5:178138800-178150400	ZNF genes & repeats	Primary B cells from cord blood	blood
34	chr5:178138800-178154400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
35	chr5:178138800-178155600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr5:178139000-178149600	ZNF genes & repeats	Fetal Lung	lung
37	chr5:178139000-178150600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
38	chr5:178139000-178150600	ZNF genes & repeats	NHEK	skin
39	chr5:178139000-178154000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
40	chr5:178139200-178144600	ZNF genes & repeats	Dnd41	blood
41	chr5:178139200-178145000	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
42	chr5:178139200-178145400	ZNF genes & repeats	Rectal Smooth Muscle	rectum
43	chr5:178139200-178149000	ZNF genes & repeats	NH-A	brain
44	chr5:178139200-178150600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
45	chr5:178139200-178150600	ZNF genes & repeats	Left Ventricle	heart
46	chr5:178139200-178150600	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
47	chr5:178139200-178150600	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
48	chr5:178139200-178150800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
49	chr5:178139400-178154800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr5:178139600-178149200	ZNF genes & repeats	Primary T cells from cord blood	blood

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