Variant report

Variant	rs28397606
Chromosome Location	chr8:87484140-87484141
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:87475541..87478210-chr8:87481447..87484239,3	K562	blood:
2	chr8:87482890..87486394-chr8:87519495..87522531,3	K562	blood:
3	chr8:87483086..87486857-chr8:87493543..87496770,3	MCF-7	breast:
4	chr8:87481910..87484178-chr8:87529355..87531387,2	MCF-7	breast:
5	chr8:87481858..87484609-chr8:87519275..87521068,2	MCF-7	breast:
6	chr8:87483608..87485189-chr8:87486909..87489201,2	K562	blood:
7	chr8:87472162..87475024-chr8:87481020..87484716,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123124	Chromatin interaction
ENSG00000176623	Chromatin interaction
ENSG00000250569	Chromatin interaction

Extended variants
information (count: 119 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs10086188	0.90[ASN][1000 genomes]
rs10089169	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10089253	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10089317	0.84[EUR][1000 genomes]
rs10090898	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10090963	0.90[ASN][1000 genomes]
rs10092168	0.87[ASN][1000 genomes]
rs10093867	0.83[EUR][1000 genomes]
rs10094332	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10095589	0.90[ASN][1000 genomes]
rs10097546	0.83[EUR][1000 genomes]
rs10097866	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10098365	0.90[ASN][1000 genomes]
rs10100182	1.00[ASN][1000 genomes]
rs10100247	0.90[ASN][1000 genomes]
rs10100254	0.97[ASN][1000 genomes]
rs10100368	1.00[ASN][1000 genomes]
rs10100698	0.84[EUR][1000 genomes]
rs10106390	0.90[ASN][1000 genomes]
rs10107117	0.90[ASN][1000 genomes]
rs10107571	0.90[ASN][1000 genomes]
rs10108586	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10109677	0.83[EUR][1000 genomes]
rs10110096	1.00[ASN][1000 genomes]
rs10110323	0.99[EUR][1000 genomes]
rs10481195	0.93[ASN][1000 genomes]
rs10504823	0.84[EUR][1000 genomes]
rs10956820	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10956821	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10956822	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10956871	0.90[ASN][1000 genomes]
rs11774253	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11774499	0.90[ASN][1000 genomes]
rs11776698	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11781993	0.83[EUR][1000 genomes]
rs11783382	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11984519	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11986423	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11994508	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11997927	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11998558	0.93[ASN][1000 genomes]
rs12155979	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12155981	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12156004	0.83[EUR][1000 genomes]
rs12216783	0.84[EUR][1000 genomes]
rs12335013	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13265266	0.82[EUR][1000 genomes]
rs16915375	0.90[ASN][1000 genomes]
rs16915389	0.90[ASN][1000 genomes]
rs17681534	0.84[EUR][1000 genomes]
rs17681826	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28384362	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28416254	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28433311	0.83[EUR][1000 genomes]
rs28438974	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28504479	0.83[EUR][1000 genomes]
rs28514445	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28540009	0.90[ASN][1000 genomes]
rs28613262	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28680173	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28687116	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28715255	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2917553	0.81[EUR][1000 genomes]
rs2953518	0.81[EUR][1000 genomes]
rs2953519	0.81[EUR][1000 genomes]
rs2976170	0.81[EUR][1000 genomes]
rs2976173	0.81[EUR][1000 genomes]
rs2976175	0.81[EUR][1000 genomes]
rs2976176	0.81[EUR][1000 genomes]
rs2976194	0.84[EUR][1000 genomes]
rs3087641	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4440616	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55671538	0.83[EUR][1000 genomes]
rs55871514	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs57638937	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58837061	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6471295	0.83[EUR][1000 genomes]
rs6471317	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6651177	0.90[ASN][1000 genomes]
rs6651268	0.90[ASN][1000 genomes]
rs67332431	1.00[ASN][1000 genomes]
rs6980476	0.90[ASN][1000 genomes]
rs6992624	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6993497	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6993612	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7015772	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7018083	0.94[ASN][1000 genomes]
rs72690416	1.00[ASN][1000 genomes]
rs72690443	0.90[ASN][1000 genomes]
rs72690445	0.90[ASN][1000 genomes]
rs72690447	0.90[ASN][1000 genomes]
rs72690455	0.90[ASN][1000 genomes]
rs72690457	0.90[ASN][1000 genomes]
rs72690474	0.90[ASN][1000 genomes]
rs73688817	0.84[EUR][1000 genomes]
rs73688823	0.83[EUR][1000 genomes]
rs73688824	0.83[EUR][1000 genomes]
rs73688827	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73688856	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73688857	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73688858	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73688859	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73688862	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7818436	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7823951	0.87[ASN][1000 genomes]
rs7824873	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7833201	0.87[ASN][1000 genomes]
rs7837581	0.83[EUR][1000 genomes]
rs7839096	0.83[EUR][1000 genomes]
rs7843272	0.84[EUR][1000 genomes]
rs7843399	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7844014	0.90[ASN][1000 genomes]
rs9297913	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9650128	0.90[ASN][1000 genomes]
rs9650129	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932023	chr8:86845979-87490694	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	esv3349873	chr8:87185763-87603726	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1023510	chr8:87429001-87874948	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv933966	chr8:87454655-87591558	ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28397606	FAM82B///LOC642197	Cis_1M	lymphoblastoid	RTeQTL
rs28397606	FAM82B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:87427600-87485600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr8:87437800-87489600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr8:87441800-87507600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr8:87444400-87488800	Weak transcription	NHLF	lung
5	chr8:87448800-87502800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr8:87451800-87485400	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr8:87453200-87488600	Weak transcription	HSMMtube	muscle
8	chr8:87453400-87492000	Strong transcription	Adipose Nuclei	Adipose
9	chr8:87457400-87507400	Weak transcription	Brain Angular Gyrus	brain
10	chr8:87457800-87492000	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr8:87458800-87486200	Strong transcription	Liver	Liver
12	chr8:87459200-87499600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr8:87460000-87485400	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr8:87460000-87492400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr8:87460600-87484400	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr8:87460600-87485000	Strong transcription	Duodenum Mucosa	Duodenum
17	chr8:87460600-87486000	Strong transcription	Dnd41	blood
18	chr8:87461000-87494200	Weak transcription	Brain Substantia Nigra	brain
19	chr8:87470000-87485800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr8:87470800-87485000	Strong transcription	Fetal Thymus	thymus
21	chr8:87471000-87497800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr8:87471800-87491600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr8:87473800-87488200	Weak transcription	Stomach Mucosa	stomach
24	chr8:87473800-87494200	Weak transcription	Brain Hippocampus Middle	brain
25	chr8:87474000-87517000	Weak transcription	Small Intestine	intestine
26	chr8:87476600-87491400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr8:87477400-87494200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr8:87477800-87494200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr8:87477800-87494600	Weak transcription	Aorta	Aorta
30	chr8:87478000-87487400	Weak transcription	Fetal Intestine Small	intestine
31	chr8:87478000-87494200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr8:87479000-87492400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr8:87479400-87486400	Strong transcription	Fetal Lung	lung
34	chr8:87479600-87499400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr8:87480000-87486400	Strong transcription	HMEC	breast
36	chr8:87480000-87491400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr8:87480600-87492000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr8:87480800-87484800	Strong transcription	Left Ventricle	heart
39	chr8:87480800-87485200	Strong transcription	GM12878-XiMat	blood
40	chr8:87480800-87485400	Strong transcription	Fetal Kidney	kidney
41	chr8:87480800-87486000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr8:87480800-87487600	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr8:87480800-87489200	Strong transcription	Primary hematopoietic stem cells	blood
44	chr8:87481000-87485600	Strong transcription	HSMM	muscle
45	chr8:87481400-87494200	Weak transcription	Right Ventricle	heart
46	chr8:87481800-87486800	Weak transcription	NH-A	brain
47	chr8:87481800-87488000	Weak transcription	Psoas Muscle	Psoas
48	chr8:87481800-87494200	Weak transcription	Gastric	stomach
49	chr8:87481800-87494800	Weak transcription	Spleen	Spleen
50	chr8:87481800-87507400	Weak transcription	Brain Inferior Temporal Lobe	brain

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