Variant report

Variant	rs2702341
Chromosome Location	chr4:56873956-56873957
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:56864492..56867321-chr4:56873422..56875435,2	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10033819	0.84[ASN][1000 genomes]
rs10033903	0.84[ASN][1000 genomes]
rs13150478	1.00[CEU][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1447048	0.91[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs1811473	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2446747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2593068	0.94[ASW][hapmap];0.89[CEU][hapmap];0.91[CHB][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.92[LWK][hapmap];0.85[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2593082	0.94[ASW][hapmap];0.89[CEU][hapmap];0.91[CHB][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.92[LWK][hapmap];0.85[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2593085	0.94[ASW][hapmap];0.91[CHB][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs2611823	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2611826	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2702325	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2702327	0.94[ASW][hapmap];0.91[CHB][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs2702328	0.83[ASN][1000 genomes]
rs2702330	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2702337	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2702338	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2702342	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2702356	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2702357	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2702359	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2951807	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4128946	0.94[ASW][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs4391104	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4479769	0.94[ASW][hapmap];0.91[CHB][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs4526032	0.94[ASW][hapmap];0.91[CHB][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs6841358	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6842522	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9884589	0.90[CHB][hapmap];0.83[JPT][hapmap];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	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	nsv427681	chr4:56651921-56908209	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2702341	CLOCK	cis	cerebellum	SCAN
rs2702341	REST	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56815800-56875000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:56816200-56884200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr4:56816200-56887800	Weak transcription	Gastric	stomach
4	chr4:56816400-56890800	Weak transcription	Colon Smooth Muscle	Colon
5	chr4:56816600-56890600	Weak transcription	Brain Hippocampus Middle	brain
6	chr4:56816600-56896400	Weak transcription	Fetal Heart	heart
7	chr4:56817400-56885400	Weak transcription	NHDF-Ad	bronchial
8	chr4:56819000-56897400	Weak transcription	HSMMtube	muscle
9	chr4:56819200-56890600	Weak transcription	NHLF	lung
10	chr4:56820600-56892400	Weak transcription	Hela-S3	cervix
11	chr4:56823600-56893800	Weak transcription	HMEC	breast
12	chr4:56828200-56884200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:56829200-56881400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr4:56829600-56890600	Weak transcription	A549	lung
15	chr4:56833000-56877200	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr4:56835400-56904800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr4:56837200-56905000	Weak transcription	Brain Substantia Nigra	brain
18	chr4:56839800-56896600	Weak transcription	Brain Angular Gyrus	brain
19	chr4:56840200-56878000	Weak transcription	NHEK	skin
20	chr4:56840200-56884600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr4:56842800-56890800	Weak transcription	Osteobl	bone
22	chr4:56844200-56891000	Weak transcription	Colonic Mucosa	Colon
23	chr4:56847200-56891000	Weak transcription	Right Ventricle	heart
24	chr4:56848800-56878000	Weak transcription	HSMM	muscle
25	chr4:56852600-56890600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr4:56853200-56876600	Weak transcription	Stomach Smooth Muscle	stomach
27	chr4:56853800-56876600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr4:56856200-56892600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr4:56856400-56889200	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr4:56857600-56897400	Strong transcription	Fetal Thymus	thymus
31	chr4:56857600-56898200	Strong transcription	Dnd41	blood
32	chr4:56857600-56898200	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr4:56858200-56889200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr4:56858800-56875000	Strong transcription	Primary hematopoietic stem cells	blood
35	chr4:56859600-56889200	Strong transcription	Primary T cells from cord blood	blood
36	chr4:56861200-56889400	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr4:56862200-56877200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr4:56863200-56892600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr4:56864600-56894200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr4:56864800-56892200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr4:56865400-56874600	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr4:56865400-56894400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr4:56866000-56883800	Weak transcription	NH-A	brain
44	chr4:56866200-56876600	Weak transcription	Liver	Liver
45	chr4:56866200-56883800	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr4:56866200-56895000	Weak transcription	Lung	lung
47	chr4:56866800-56876400	Weak transcription	Placenta	Placenta
48	chr4:56866800-56878200	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr4:56866800-56878600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr4:56866800-56878600	Weak transcription	K562	blood

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