Variant report

Variant	rs10060764
Chromosome Location	chr5:178369673-178369674
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10043049	0.92[ASN][1000 genomes]
rs10044980	0.88[ASN][1000 genomes]
rs10074870	0.92[CEU][hapmap];0.91[GIH][hapmap];0.82[EUR][1000 genomes]
rs10075112	0.95[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11747215	0.88[ASN][1000 genomes]
rs12514348	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2016212	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4700752	0.95[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4700753	0.95[ASN][1000 genomes]
rs4700971	0.95[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs57272473	0.94[ASN][1000 genomes]
rs903981	0.89[CEU][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv600489	chr5:178368096-178430375	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10060764	GFPT2	cis	parietal	SCAN
rs10060764	ZNF454	cis	parietal	SCAN
rs10060764	ZFP2	cis	parietal	SCAN
rs10060764	N4BP3	cis	parietal	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178353800-178374800	ZNF genes & repeats	Liver	Liver
2	chr5:178366000-178370200	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
3	chr5:178366400-178372600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:178366800-178370200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
5	chr5:178366800-178370200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
6	chr5:178366800-178370400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr5:178367000-178370400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
8	chr5:178367000-178374600	ZNF genes & repeats	Spleen	Spleen
9	chr5:178367400-178369800	Active TSS	Rectal Smooth Muscle	rectum
10	chr5:178367400-178370600	ZNF genes & repeats	Fetal Intestine Large	intestine
11	chr5:178368400-178370400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr5:178368600-178370200	ZNF genes & repeats	Fetal Intestine Small	intestine
13	chr5:178368800-178370000	ZNF genes & repeats	Placenta	Placenta
14	chr5:178368800-178370400	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:178368800-178377000	Weak transcription	Psoas Muscle	Psoas
16	chr5:178369000-178369800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr5:178369000-178369800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr5:178369000-178370000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr5:178369000-178370200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr5:178369000-178371000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr5:178369000-178371200	Weak transcription	Brain Angular Gyrus	brain
22	chr5:178369000-178371200	Weak transcription	Fetal Kidney	kidney
23	chr5:178369000-178371200	Weak transcription	Left Ventricle	heart
24	chr5:178369000-178372800	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr5:178369000-178373800	Weak transcription	Brain Substantia Nigra	brain
26	chr5:178369000-178374000	Weak transcription	Osteobl	bone
27	chr5:178369000-178374400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
28	chr5:178369000-178378400	Weak transcription	NHDF-Ad	bronchial
29	chr5:178369000-178378800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr5:178369000-178380200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr5:178369000-178384800	ZNF genes & repeats	Fetal Stomach	stomach
32	chr5:178369200-178370200	Weak transcription	Brain Anterior Caudate	brain
33	chr5:178369200-178370200	Weak transcription	Pancreas	Pancrea
34	chr5:178369200-178371200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr5:178369200-178371200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr5:178369200-178371800	Weak transcription	Fetal Heart	heart
37	chr5:178369200-178372200	Weak transcription	Right Ventricle	heart
38	chr5:178369200-178373000	Weak transcription	Colon Smooth Muscle	Colon
39	chr5:178369400-178369800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr5:178369400-178370000	Active TSS	Primary T cells from cord blood	blood
41	chr5:178369400-178370000	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr5:178369400-178374800	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr5:178369400-178418200	ZNF genes & repeats	Fetal Brain Female	brain
44	chr5:178369600-178370200	ZNF genes & repeats	Esophagus	oesophagus
45	chr5:178369600-178370200	Weak transcription	Ovary	ovary
46	chr5:178369600-178370600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr5:178369600-178370600	ZNF genes & repeats	Fetal Brain Male	brain
48	chr5:178369600-178370600	ZNF genes & repeats	Fetal Muscle Leg	muscle
49	chr5:178369600-178370800	ZNF genes & repeats	Brain Hippocampus Middle	brain
50	chr5:178369600-178372200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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