Variant report

Variant	rs2412720
Chromosome Location	chr4:56927056-56927057
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10517367	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11729231	0.86[EUR][1000 genomes]
rs11938852	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13112752	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17086249	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2412721	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2412722	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412725	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2412726	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2899054	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34546346	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34577487	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35204688	0.85[EUR][1000 genomes]
rs35976456	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36092812	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4355456	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4645275	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58927874	0.85[EUR][1000 genomes]
rs59053231	0.96[ASN][1000 genomes]
rs59838410	0.89[ASN][1000 genomes]
rs60296378	0.89[ASN][1000 genomes]
rs6819574	0.93[ASN][1000 genomes]
rs6826903	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6836376	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6839870	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73155600	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73155601	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73162699	0.98[ASN][1000 genomes]
rs73162701	0.93[ASN][1000 genomes]
rs7659294	0.85[EUR][1000 genomes]
rs7661471	0.83[EUR][1000 genomes]
rs7672541	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7676365	0.95[ASN][1000 genomes]
rs7681714	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755990	chr4:56317136-57143037	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv1005845	chr4:56522075-56980357	Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2412720	CLOCK	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56916400-56936200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr4:56916600-56929400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:56916600-56931600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr4:56916600-56934200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:56917200-56934600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr4:56922000-56927200	Weak transcription	Fetal Brain Male	brain
7	chr4:56922000-56934200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr4:56922000-56934400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr4:56922000-56935600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr4:56922200-56928600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr4:56922200-56934000	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr4:56922200-56935000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr4:56922800-56934000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr4:56922800-56934200	Weak transcription	Fetal Stomach	stomach
15	chr4:56922800-56934800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr4:56923400-56928000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:56923800-56928400	Weak transcription	HepG2	liver
18	chr4:56923800-56936400	Weak transcription	Fetal Intestine Small	intestine
19	chr4:56923800-56936800	Weak transcription	Fetal Intestine Large	intestine
20	chr4:56925000-56928800	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr4:56925200-56928200	Weak transcription	Fetal Lung	lung
22	chr4:56925200-56932800	Weak transcription	Brain Germinal Matrix	brain
23	chr4:56925200-56933400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr4:56925400-56927400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr4:56925600-56928200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr4:56925800-56928800	Weak transcription	Fetal Brain Female	brain
27	chr4:56926200-56927400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr4:56926600-56928600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr4:56926800-56927200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr4:56926800-56927200	Weak transcription	Fetal Muscle Leg	muscle
31	chr4:56926800-56936200	Weak transcription	Fetal Kidney	kidney
32	chr4:56927000-56928600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr4:56927000-56930000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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