Variant report

Variant	rs1108907
Chromosome Location	chr4:79543342-79543343
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:79542792..79544409-chr4:79720591..79722991,2	K562	blood:
2	chr4:79542556..79545467-chr4:79549942..79551796,4	K562	blood:
3	chr4:79541751..79544197-chr4:79672798..79674957,2	K562	blood:
4	chr4:79539469..79541784-chr4:79542967..79545654,2	K562	blood:
5	chr4:79542135..79543835-chr4:79696939..79698842,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138756	Chromatin interaction
ENSG00000260278	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:74)

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	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10212636	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1107606	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11724268	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11724602	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11728013	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11731482	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11733032	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[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];0.86[EUR][1000 genomes]
rs11736376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[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];0.83[AMR][1000 genomes];0.87[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];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12233694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12233707	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12643488	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12646646	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12650411	0.87[EUR][1000 genomes]
rs12711032	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[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];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13138005	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs1972024	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28597797	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34325799	0.83[EUR][1000 genomes]
rs4073678	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4073679	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4074673	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4074674	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4075927	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4077709	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4270605	0.82[AMR][1000 genomes];0.83[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];0.81[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4353930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4632683	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4643844	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4975148	0.96[EUR][1000 genomes]
rs6533821	0.90[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6533825	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6533835	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[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];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6533847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6811335	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6811782	0.88[JPT][hapmap]
rs6812227	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6812441	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6814739	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6819484	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6824014	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6829061	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6829198	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6834587	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6835210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6835998	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6836513	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6838443	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AMR][1000 genomes];0.82[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];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6841654	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6845893	0.88[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.86[TSI][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6846346	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6851341	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6854055	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]
rs6858740	0.88[JPT][hapmap]
rs7317	0.94[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7657082	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7669674	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7669866	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7670506	0.87[EUR][1000 genomes]
rs7680749	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7680766	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];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7682984	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7689154	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7697461	0.86[EUR][1000 genomes]
rs9998136	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[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
rs1108907	PRDM8	cis	parietal	SCAN
rs1108907	LOC643424	cis	multi-tissue	Pritchard
rs1108907	ART3	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79518000-79548000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr4:79518600-79543600	Weak transcription	Stomach Mucosa	stomach
3	chr4:79524200-79543400	Weak transcription	A549	lung
4	chr4:79533800-79548800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr4:79534600-79547800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:79536400-79550600	Weak transcription	Left Ventricle	heart
7	chr4:79537000-79545800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr4:79537800-79543400	Weak transcription	HSMM	muscle
9	chr4:79539200-79549800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr4:79539400-79550400	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr4:79539600-79550000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr4:79539800-79545200	Weak transcription	GM12878-XiMat	blood
13	chr4:79540200-79543400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr4:79542200-79543600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr4:79542200-79555600	Enhancers	Fetal Intestine Small	intestine
16	chr4:79542400-79543400	Flanking Active TSS	K562	blood
17	chr4:79542600-79544000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr4:79542600-79544000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr4:79542600-79544000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr4:79542600-79544200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr4:79542600-79544200	Enhancers	NHDF-Ad	bronchial
22	chr4:79542600-79544200	Enhancers	NHLF	lung
23	chr4:79542600-79544400	Enhancers	NH-A	brain
24	chr4:79542600-79555600	Enhancers	Fetal Intestine Large	intestine
25	chr4:79542800-79543400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr4:79542800-79544000	Enhancers	HSMMtube	muscle
27	chr4:79542800-79546000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr4:79543000-79544000	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr4:79543000-79544000	Enhancers	HepG2	liver
30	chr4:79543000-79544200	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr4:79543000-79544200	Enhancers	Placenta Amnion	Placenta Amnion
32	chr4:79543000-79544200	Enhancers	Hela-S3	cervix
33	chr4:79543000-79544400	Enhancers	Osteobl	bone
34	chr4:79543000-79545600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr4:79543200-79543600	Weak transcription	Placenta	Placenta
36	chr4:79543200-79543800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr4:79543200-79544000	Enhancers	Right Atrium	heart
38	chr4:79543200-79544200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr4:79543200-79544400	Enhancers	HUVEC	blood vessel

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