Variant report

Variant	rs2412723
Chromosome Location	chr4:56951767-56951768
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1108947	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1108948	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11721368	0.93[ASN][1000 genomes]
rs11729231	0.91[ASN][1000 genomes]
rs11934389	0.93[ASN][1000 genomes]
rs13102087	0.93[ASN][1000 genomes]
rs13109242	0.86[ASN][1000 genomes]
rs13113844	0.93[ASN][1000 genomes]
rs13121092	0.93[ASN][1000 genomes]
rs13139132	0.82[ASN][1000 genomes]
rs13147381	0.92[ASN][1000 genomes]
rs2412717	0.93[ASN][1000 genomes]
rs2412718	0.93[ASN][1000 genomes]
rs2412719	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs34181414	0.93[ASN][1000 genomes]
rs34683632	0.91[ASN][1000 genomes]
rs34796075	0.93[ASN][1000 genomes]
rs35204688	0.91[ASN][1000 genomes]
rs35400594	0.93[ASN][1000 genomes]
rs35417087	0.88[ASN][1000 genomes]
rs35770075	0.93[ASN][1000 genomes]
rs35786306	0.93[ASN][1000 genomes]
rs35786805	0.93[ASN][1000 genomes]
rs4364320	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs58795379	0.93[ASN][1000 genomes]
rs58927874	0.91[ASN][1000 genomes]
rs6554328	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6839220	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs71601617	0.93[ASN][1000 genomes]
rs7657181	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7659294	0.91[ASN][1000 genomes]
rs7659694	0.93[ASN][1000 genomes]
rs7661471	0.98[ASN][1000 genomes]
rs7663270	0.93[ASN][1000 genomes]
rs7681714	0.95[ASN][1000 genomes]
rs7685766	0.98[ASN][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	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
3	nsv999328	chr4:56942917-57041586	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1007114	chr4:56942917-57055381	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2412723	CLOCK	cis	parietal	SCAN
rs2412723	CTSA	trans	cerebellum	SCAN
rs2412723	KDR	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56945200-56951800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr4:56945400-56952200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:56945600-56965200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr4:56947000-56951800	Weak transcription	Fetal Intestine Small	intestine
5	chr4:56947600-56952200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr4:56947800-56957000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr4:56948800-56972200	Weak transcription	Fetal Stomach	stomach
8	chr4:56949000-56965200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr4:56949600-56952200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr4:56950800-56952800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:56950800-56952800	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr4:56951000-56952600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr4:56951000-56952800	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr4:56951000-56952800	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr4:56951000-56952800	Enhancers	Fetal Kidney	kidney
16	chr4:56951000-56953000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr4:56951000-56953200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr4:56951000-56953200	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr4:56951000-56953600	Enhancers	Brain Germinal Matrix	brain
20	chr4:56951200-56952000	Enhancers	Fetal Brain Female	brain
21	chr4:56951200-56952000	Flanking Active TSS	Hela-S3	cervix
22	chr4:56951200-56952200	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr4:56951200-56952600	Enhancers	H9 Cell Line	embryonic stem cell
24	chr4:56951200-56952800	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr4:56951200-56952800	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr4:56951200-56953000	Enhancers	H1 Cell Line	embryonic stem cell
27	chr4:56951400-56952000	Weak transcription	Brain Anterior Caudate	brain
28	chr4:56951400-56952200	Weak transcription	Ovary	ovary
29	chr4:56951400-56952200	Weak transcription	Right Atrium	heart
30	chr4:56951400-56952400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr4:56951400-56952600	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr4:56951400-56952600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr4:56951600-56951800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr4:56951600-56951800	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr4:56951600-56952000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr4:56951600-56952000	Weak transcription	Stomach Mucosa	stomach
37	chr4:56951600-56952400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr4:56951600-56952400	Enhancers	Duodenum Mucosa	Duodenum
39	chr4:56951600-56952400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr4:56951600-56952400	Enhancers	Fetal Muscle Leg	muscle

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