Variant report

Variant	rs2593068
Chromosome Location	chr4:56829482-56829483
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	chr4:56814955..56816833-chr4:56828456..56830124,2	K562	blood:
2	chr4:56820475..56822078-chr4:56827472..56830252,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174799	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10033819	0.95[ASN][1000 genomes]
rs10033903	0.96[ASN][1000 genomes]
rs13150478	0.88[CEU][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1447048	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1811473	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2446747	0.89[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2593082	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2593085	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2611823	0.88[ASW][hapmap];0.89[CEU][hapmap];0.91[CHB][hapmap];0.89[GIH][hapmap];0.87[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2611826	0.88[ASW][hapmap];0.89[CEU][hapmap];0.91[CHB][hapmap];0.89[GIH][hapmap];0.87[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2702325	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2702327	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2702328	0.97[ASN][1000 genomes]
rs2702330	0.88[ASW][hapmap];0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2702337	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2702338	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2702341	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]
rs2702342	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2702356	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2702357	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2702359	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2951807	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4128946	0.88[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4391104	0.88[ASW][hapmap];0.89[CEU][hapmap];0.86[CHB][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4479769	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4526032	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4865048	0.90[ASN][1000 genomes]
rs6838426	0.86[JPT][hapmap]
rs6841358	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6842522	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9884589	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv10496	chr4:56336946-56841137	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	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
4	esv3406311	chr4:56580578-56840877	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	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
rs2593068	REST	cis	parietal	SCAN
rs2593068	CLOCK	cis	cerebellum	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56815800-56839200	Weak transcription	Esophagus	oesophagus
2	chr4:56815800-56875000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:56816000-56833400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr4:56816200-56839400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:56816200-56846600	Weak transcription	Right Ventricle	heart
6	chr4:56816200-56873400	Weak transcription	Pancreas	Pancrea
7	chr4:56816200-56884200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr4:56816200-56887800	Weak transcription	Gastric	stomach
9	chr4:56816400-56866000	Weak transcription	Spleen	Spleen
10	chr4:56816400-56890800	Weak transcription	Colon Smooth Muscle	Colon
11	chr4:56816600-56829800	Weak transcription	Colonic Mucosa	Colon
12	chr4:56816600-56831800	Weak transcription	Fetal Lung	lung
13	chr4:56816600-56834000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr4:56816600-56851800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr4:56816600-56852000	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr4:56816600-56865800	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr4:56816600-56890600	Weak transcription	Brain Hippocampus Middle	brain
18	chr4:56816600-56896400	Weak transcription	Fetal Heart	heart
19	chr4:56816800-56831400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr4:56816800-56865800	Weak transcription	Small Intestine	intestine
21	chr4:56816800-56869800	Weak transcription	HepG2	liver
22	chr4:56817400-56839200	Weak transcription	NHEK	skin
23	chr4:56817400-56885400	Weak transcription	NHDF-Ad	bronchial
24	chr4:56817800-56846200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr4:56817800-56854600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr4:56818200-56837200	Strong transcription	Fetal Thymus	thymus
27	chr4:56818200-56853800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr4:56818400-56829800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr4:56818400-56831000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr4:56818400-56833000	Strong transcription	Primary B cells from peripheral blood	blood
31	chr4:56818800-56841800	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr4:56819000-56835400	Strong transcription	Dnd41	blood
33	chr4:56819000-56897400	Weak transcription	HSMMtube	muscle
34	chr4:56819200-56859600	Weak transcription	Fetal Kidney	kidney
35	chr4:56819200-56890600	Weak transcription	NHLF	lung
36	chr4:56820000-56841600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr4:56820400-56829600	Strong transcription	Primary T cells from cord blood	blood
38	chr4:56820600-56892400	Weak transcription	Hela-S3	cervix
39	chr4:56821600-56831400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr4:56822200-56849800	Weak transcription	Fetal Brain Male	brain
41	chr4:56822200-56873600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr4:56822400-56845000	Weak transcription	K562	blood
43	chr4:56822400-56865800	Weak transcription	Psoas Muscle	Psoas
44	chr4:56823600-56893800	Weak transcription	HMEC	breast
45	chr4:56824000-56846600	Weak transcription	Stomach Smooth Muscle	stomach
46	chr4:56824200-56832000	Weak transcription	Liver	Liver
47	chr4:56824200-56834200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr4:56824600-56830000	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr4:56824600-56838400	Weak transcription	Fetal Brain Female	brain
50	chr4:56824600-56839600	Weak transcription	H1 Cell Line	embryonic stem cell

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