Variant report

Variant	rs4306980
Chromosome Location	chr4:79536003-79536004
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:79534997..79539335-chr4:79548255..79551176,6	K562	blood:
2	chr4:79533816..79536159-chr4:79571823..79573589,2	K562	blood:
3	chr4:79534869..79536499-chr4:79696257..79698804,3	MCF-7	breast:
4	chr4:79531270..79533503-chr4:79534064..79536623,2	MCF-7	breast:
5	chr4:79534010..79538453-chr4:79546769..79551125,4	K562	blood:
6	chr4:79534658..79536722-chr4:79591597..79593371,2	K562	blood:

Variant related genes	Relation type
ENSG00000260278	Chromatin interaction
ENSG00000138756	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10001246	0.90[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10007186	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs10019240	0.83[EUR][1000 genomes]
rs10212636	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1107606	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1108907	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11724268	1.00[CEU][hapmap];0.82[CHB][hapmap];0.97[GIH][hapmap];0.96[MEX][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11724602	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11728013	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11731482	0.83[EUR][1000 genomes]
rs11733032	0.95[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11733269	0.90[CEU][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs11736376	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11736602	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11942573	0.90[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs12233694	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12233707	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12643488	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12646646	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12650411	0.87[EUR][1000 genomes]
rs12711032	0.90[CEU][hapmap];0.82[CHB][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13120630	0.90[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs13138005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1972024	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28597797	0.86[EUR][1000 genomes]
rs34325799	0.83[EUR][1000 genomes]
rs4073678	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4073679	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4074673	0.83[EUR][1000 genomes]
rs4074674	0.83[EUR][1000 genomes]
rs4075927	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4077709	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4270605	0.83[EUR][1000 genomes]
rs4353930	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4632683	0.82[EUR][1000 genomes]
rs4643844	0.83[EUR][1000 genomes]
rs4975148	0.96[EUR][1000 genomes]
rs6533821	0.90[CEU][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6533825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6533835	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6533842	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6533847	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs6811335	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6812227	0.83[EUR][1000 genomes]
rs6812441	0.89[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs6814739	0.87[EUR][1000 genomes]
rs6819484	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6824014	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6829061	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6829198	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6834587	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6835210	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6835998	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6836513	0.83[EUR][1000 genomes]
rs6838443	0.90[CEU][hapmap];0.82[CHB][hapmap];0.82[EUR][1000 genomes]
rs6840592	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6841654	1.00[CEU][hapmap]
rs6845893	0.90[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs6846346	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6851341	0.87[EUR][1000 genomes]
rs6854055	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]
rs7317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7657082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7669674	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7669866	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7670506	0.87[EUR][1000 genomes]
rs7680749	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7680766	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7682984	0.81[EUR][1000 genomes]
rs7689154	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7697461	0.86[EUR][1000 genomes]
rs9998136	0.93[CEU][hapmap];0.82[CHB][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4306980	PRDM8	cis	parietal	SCAN
rs4306980	ART3	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79491800-79542600	Weak transcription	NH-A	brain
2	chr4:79512600-79536800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr4:79518000-79548000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr4:79518600-79543600	Weak transcription	Stomach Mucosa	stomach
5	chr4:79524200-79543400	Weak transcription	A549	lung
6	chr4:79527800-79542600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:79527800-79542600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr4:79529400-79537600	Enhancers	Dnd41	blood
9	chr4:79529800-79536200	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr4:79529800-79537000	Enhancers	Primary hematopoietic stem cells	blood
11	chr4:79530000-79540000	Enhancers	Primary T cells from cord blood	blood
12	chr4:79531200-79536600	Enhancers	Primary B cells from cord blood	blood
13	chr4:79531200-79536800	Enhancers	Primary B cells from peripheral blood	blood
14	chr4:79531400-79543000	Weak transcription	Hela-S3	cervix
15	chr4:79531800-79543200	Weak transcription	HUVEC	blood vessel
16	chr4:79532000-79536800	Enhancers	Fetal Thymus	thymus
17	chr4:79532000-79537200	Weak transcription	HSMM	muscle
18	chr4:79532400-79536800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr4:79532400-79537200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr4:79532400-79537200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr4:79532600-79537200	Weak transcription	NHDF-Ad	bronchial
22	chr4:79533000-79536200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr4:79533200-79536800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr4:79533800-79538600	Enhancers	Fetal Intestine Large	intestine
25	chr4:79533800-79541000	Enhancers	Fetal Intestine Small	intestine
26	chr4:79533800-79548800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr4:79534200-79537200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr4:79534200-79537200	Weak transcription	HMEC	breast
29	chr4:79534200-79537200	Weak transcription	NHEK	skin
30	chr4:79534600-79536800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr4:79534600-79547800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr4:79534800-79537000	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr4:79534800-79538200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr4:79535000-79536200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr4:79535000-79536200	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr4:79535200-79536400	Enhancers	Left Ventricle	heart
37	chr4:79535200-79538000	Enhancers	K562	blood
38	chr4:79535400-79536400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr4:79535400-79542600	Weak transcription	Placenta	Placenta
40	chr4:79535600-79539200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr4:79535600-79543000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr4:79535800-79536800	Enhancers	GM12878-XiMat	blood
43	chr4:79536000-79536600	Weak transcription	Thymus	Thymus
44	chr4:79536000-79536800	Enhancers	Fetal Heart	heart

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