Variant report

Variant	rs6854055
Chromosome Location	chr4:79551592-79551593
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:79542556..79545467-chr4:79549942..79551796,4	K562	blood:
2	chr4:79549970..79552473-chr4:79560389..79564299,4	K562	blood:
3	chr4:79549841..79552363-chr4:79696027..79698127,2	MCF-7	breast:
4	chr4:79547404..79551814-chr4:79694410..79698430,6	K562	blood:
5	chr4:79550103..79553175-chr4:79717288..79720915,3	K562	blood:
6	chr4:79549184..79553600-chr4:79560172..79565329,6	K562	blood:
7	chr4:79547404..79553256-chr4:79694666..79698430,7	K562	blood:

Variant related genes	Relation type
ENSG00000238816	Chromatin interaction
ENSG00000260278	Chromatin interaction
ENSG00000138756	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10001246	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs10007186	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs10019240	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10212636	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1107606	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1108907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11724268	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11724602	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11728013	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11731482	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11733032	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11733269	0.90[CEU][hapmap];0.94[GIH][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs11736376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11736602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11942573	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12233694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12233707	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12643488	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12646646	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12650411	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12711032	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13120630	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13138005	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs1972024	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28597797	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34325799	0.86[EUR][1000 genomes]
rs4073678	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4073679	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4074673	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4074674	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4075927	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4077709	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4270605	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4306980	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4353930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4632683	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4643844	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4975148	0.99[EUR][1000 genomes]
rs6533821	0.90[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs6533825	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6533835	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6533842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6533845	0.81[AMR][1000 genomes]
rs6533847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6811335	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6811782	0.88[JPT][hapmap]
rs6812227	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6812441	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6814739	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6819484	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6824014	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6829061	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6829198	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6834587	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6835210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6835998	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6836513	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6838443	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6840592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6841654	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6845893	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6846346	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6851341	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6858740	0.88[JPT][hapmap]
rs7317	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7657082	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7669674	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7669866	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7670506	0.89[EUR][1000 genomes]
rs7680749	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7680766	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7682984	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7689154	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7697461	0.89[EUR][1000 genomes]
rs9998136	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6854055	LOC643424	cis	multi-tissue	Pritchard
rs6854055	ART3	cis	parietal	SCAN
rs6854055	PRDM8	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79542200-79555600	Enhancers	Fetal Intestine Small	intestine
2	chr4:79542600-79555600	Enhancers	Fetal Intestine Large	intestine
3	chr4:79546600-79553000	Enhancers	Placenta	Placenta
4	chr4:79547600-79551800	Enhancers	Stomach Mucosa	stomach
5	chr4:79548000-79551800	Enhancers	HepG2	liver
6	chr4:79548000-79553200	Enhancers	Placenta Amnion	Placenta Amnion
7	chr4:79548200-79552600	Enhancers	Duodenum Mucosa	Duodenum
8	chr4:79548200-79555000	Weak transcription	Osteobl	bone
9	chr4:79548600-79553600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr4:79548800-79552200	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr4:79548800-79557400	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr4:79549600-79551800	Weak transcription	Small Intestine	intestine
13	chr4:79549600-79560000	Weak transcription	HMEC	breast
14	chr4:79549800-79551600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
15	chr4:79549800-79551600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr4:79549800-79551600	Enhancers	Fetal Kidney	kidney
17	chr4:79549800-79552000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr4:79549800-79552000	Enhancers	Pancreatic Islets	Pancreatic Islet
19	chr4:79549800-79554200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr4:79550000-79551600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr4:79550000-79552000	Enhancers	Hela-S3	cervix
22	chr4:79550000-79552200	Enhancers	Rectal Mucosa Donor 29	rectum
23	chr4:79550000-79552800	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr4:79550200-79551600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr4:79550200-79552000	Enhancers	Brain Anterior Caudate	brain
26	chr4:79550200-79552200	Enhancers	Primary hematopoietic stem cells	blood
27	chr4:79550200-79553200	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr4:79550200-79556600	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr4:79550400-79555000	Weak transcription	NHDF-Ad	bronchial
30	chr4:79550400-79564200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr4:79550600-79551600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr4:79550600-79552200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr4:79550600-79552800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
34	chr4:79551200-79551600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
35	chr4:79551200-79551600	Enhancers	Adipose Nuclei	Adipose
36	chr4:79551200-79551800	Enhancers	Colonic Mucosa	Colon
37	chr4:79551200-79552400	Flanking Active TSS	GM12878-XiMat	blood
38	chr4:79551200-79554200	Weak transcription	Brain Hippocampus Middle	brain
39	chr4:79551200-79554400	Weak transcription	Brain Substantia Nigra	brain
40	chr4:79551400-79551600	Flanking Active TSS	Primary B cells from cord blood	blood
41	chr4:79551400-79552200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr4:79551400-79553200	Enhancers	K562	blood
43	chr4:79551400-79553600	Weak transcription	Left Ventricle	heart
44	chr4:79551400-79553600	Weak transcription	Pancreas	Pancrea
45	chr4:79551400-79555200	Weak transcription	Right Atrium	heart
46	chr4:79551400-79558400	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr4:79551400-79578200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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