Variant report

Variant	rs28687116
Chromosome Location	chr8:87528418-87528419
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CUX1	chr8:87527706-87528590	GM12878	blood:	n/a	n/a
2	IRF4	chr8:87527854-87528436	GM12878	blood:	n/a	n/a
3	MEF2A	chr8:87527749-87528430	GM12878	blood:	n/a	chr8:87528014-87528035 chr8:87528015-87528031 chr8:87528018-87528029 chr8:87528280-87528288 chr8:87528016-87528031 chr8:87528015-87528032 chr8:87528017-87528028 chr8:87528266-87528281 chr8:87528019-87528028 chr8:87528019-87528030 chr8:87528016-87528032 chr8:87528014-87528035 chr8:87528014-87528035
4	RUNX3	chr8:87527648-87528529	GM12878	blood:	n/a	n/a
5	RUNX3	chr8:87527880-87528475	GM12878	blood:	n/a	n/a
6	POLR2A	chr8:87528410-87528475	MCF10A-Er-Src	breast:	n/a	n/a
7	MTA3	chr8:87527762-87528449	GM12878	blood:	n/a	n/a
8	POLR2A	chr8:87526343-87528647	GM12878	blood:	n/a	n/a
9	TBL1XR1	chr8:87527588-87528462	GM12878	blood:	n/a	n/a
10	EBF1	chr8:87527881-87528600	GM12878	blood:	n/a	n/a
11	SPI1	chr8:87527568-87528568	GM12878	blood:	n/a	chr8:87528164-87528173
12	FOXM1	chr8:87527897-87528423	GM12878	blood:	n/a	n/a
13	NFIC	chr8:87527684-87528472	GM12878	blood:	n/a	n/a
14	SPI1	chr8:87527900-87528431	GM12891	blood:	n/a	chr8:87528164-87528173
15	NFIC	chr8:87527789-87528593	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
RMDN1	TF binding region

Extended variants
information (count: 109 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10086188	1.00[ASN][1000 genomes]
rs10089169	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10089253	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10089317	0.82[EUR][1000 genomes]
rs10090898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10090963	1.00[ASN][1000 genomes]
rs10093867	0.81[EUR][1000 genomes]
rs10094332	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10095589	1.00[ASN][1000 genomes]
rs10097546	0.81[EUR][1000 genomes]
rs10097866	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10098365	1.00[ASN][1000 genomes]
rs10100182	0.90[ASN][1000 genomes]
rs10100247	1.00[ASN][1000 genomes]
rs10100254	0.88[ASN][1000 genomes]
rs10100368	0.90[ASN][1000 genomes]
rs10100698	0.82[EUR][1000 genomes]
rs10106390	1.00[ASN][1000 genomes]
rs10107117	1.00[ASN][1000 genomes]
rs10107571	1.00[ASN][1000 genomes]
rs10108586	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10109677	0.81[EUR][1000 genomes]
rs10110096	0.90[ASN][1000 genomes]
rs10110323	0.98[EUR][1000 genomes]
rs10481195	0.84[ASN][1000 genomes]
rs10504823	0.82[EUR][1000 genomes]
rs10956820	0.85[EUR][1000 genomes]
rs10956821	0.83[EUR][1000 genomes]
rs10956822	0.85[EUR][1000 genomes]
rs10956871	1.00[ASN][1000 genomes]
rs11774253	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11774499	1.00[ASN][1000 genomes]
rs11776698	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11781993	0.81[EUR][1000 genomes]
rs11783382	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11984519	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11986423	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11994508	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11997927	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11998558	0.84[ASN][1000 genomes]
rs12155979	0.88[EUR][1000 genomes]
rs12155981	0.88[EUR][1000 genomes]
rs12156004	0.81[EUR][1000 genomes]
rs12216783	0.82[EUR][1000 genomes]
rs12335013	0.84[EUR][1000 genomes]
rs16915375	1.00[ASN][1000 genomes]
rs16915389	1.00[ASN][1000 genomes]
rs17681534	0.82[EUR][1000 genomes]
rs17681826	0.84[EUR][1000 genomes]
rs28384362	0.87[EUR][1000 genomes]
rs28397606	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28416254	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28433311	0.81[EUR][1000 genomes]
rs28438974	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28504479	0.81[EUR][1000 genomes]
rs28514445	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28540009	1.00[ASN][1000 genomes]
rs28613262	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28680173	0.88[EUR][1000 genomes]
rs28715255	0.84[EUR][1000 genomes]
rs2976194	0.82[EUR][1000 genomes]
rs3087641	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4440616	0.91[EUR][1000 genomes]
rs55671538	0.81[EUR][1000 genomes]
rs55871514	0.85[EUR][1000 genomes]
rs57638937	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58837061	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6471295	0.81[EUR][1000 genomes]
rs6471317	0.85[EUR][1000 genomes]
rs6651177	1.00[ASN][1000 genomes]
rs6651268	1.00[ASN][1000 genomes]
rs67332431	0.90[ASN][1000 genomes]
rs6980476	1.00[ASN][1000 genomes]
rs6992624	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6993497	0.85[EUR][1000 genomes]
rs6993612	0.84[EUR][1000 genomes]
rs7015772	0.84[EUR][1000 genomes]
rs7018083	0.85[ASN][1000 genomes]
rs72690416	0.90[ASN][1000 genomes]
rs72690443	1.00[ASN][1000 genomes]
rs72690445	1.00[ASN][1000 genomes]
rs72690447	1.00[ASN][1000 genomes]
rs72690455	1.00[ASN][1000 genomes]
rs72690457	1.00[ASN][1000 genomes]
rs72690474	1.00[ASN][1000 genomes]
rs73688817	0.82[EUR][1000 genomes]
rs73688823	0.81[EUR][1000 genomes]
rs73688824	0.81[EUR][1000 genomes]
rs73688827	0.84[EUR][1000 genomes]
rs73688856	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73688857	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73688858	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73688859	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73688862	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7818436	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7823951	0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7824873	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7833201	0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7837581	0.81[EUR][1000 genomes]
rs7839096	0.80[EUR][1000 genomes]
rs7843272	0.82[EUR][1000 genomes]
rs7843399	0.87[EUR][1000 genomes]
rs7844014	1.00[ASN][1000 genomes]
rs9297913	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9650128	1.00[ASN][1000 genomes]
rs9650129	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
rs28687116	FAM82B///LOC642197	Cis_1M	lymphoblastoid	RTeQTL
rs28687116	FAM82B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:87527200-87528600	Enhancers	Spleen	Spleen
2	chr8:87527200-87528600	Flanking Active TSS	GM12878-XiMat	blood
3	chr8:87527400-87528600	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr8:87527400-87528600	Enhancers	Primary B cells from peripheral blood	blood
5	chr8:87527400-87568400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr8:87527600-87528600	Enhancers	Small Intestine	intestine
7	chr8:87527600-87528800	Enhancers	Primary B cells from cord blood	blood
8	chr8:87527600-87530400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr8:87527600-87530600	Enhancers	Primary hematopoietic stem cells	blood
10	chr8:87527600-87534600	Weak transcription	Placenta	Placenta
11	chr8:87527600-87534800	Weak transcription	HSMM	muscle
12	chr8:87527600-87535000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr8:87527600-87539400	Weak transcription	Lung	lung
14	chr8:87527600-87542400	Weak transcription	Esophagus	oesophagus
15	chr8:87527600-87550200	Weak transcription	Aorta	Aorta
16	chr8:87527600-87562000	Weak transcription	Pancreas	Pancrea
17	chr8:87527600-87568200	Weak transcription	Gastric	stomach
18	chr8:87527600-87584000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr8:87527800-87528600	Enhancers	Brain Hippocampus Middle	brain
20	chr8:87527800-87528600	Flanking Active TSS	Fetal Heart	heart
21	chr8:87527800-87528600	Enhancers	Fetal Intestine Large	intestine
22	chr8:87527800-87528800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr8:87527800-87528800	Strong transcription	Fetal Muscle Trunk	muscle
24	chr8:87527800-87529400	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr8:87527800-87535400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr8:87527800-87541600	Weak transcription	Ovary	ovary
27	chr8:87527800-87542600	Weak transcription	A549	lung
28	chr8:87527800-87543400	Weak transcription	K562	blood
29	chr8:87527800-87546200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr8:87527800-87546200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr8:87527800-87547400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr8:87527800-87560000	Weak transcription	HSMMtube	muscle
33	chr8:87528000-87528600	Genic enhancers	Primary T cells from cord blood	blood
34	chr8:87528000-87528600	Enhancers	Brain Substantia Nigra	brain
35	chr8:87528000-87528600	Genic enhancers	NHEK	skin
36	chr8:87528000-87528600	Enhancers	NHLF	lung
37	chr8:87528000-87530000	Weak transcription	Osteobl	bone
38	chr8:87528000-87530400	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr8:87528000-87534400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr8:87528000-87534800	Weak transcription	Liver	Liver
41	chr8:87528000-87535000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr8:87528000-87535000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr8:87528000-87539200	Weak transcription	Brain Germinal Matrix	brain
44	chr8:87528000-87541600	Weak transcription	Fetal Brain Female	brain
45	chr8:87528000-87543200	Weak transcription	Fetal Kidney	kidney
46	chr8:87528000-87543200	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr8:87528000-87550800	Weak transcription	Psoas Muscle	Psoas
48	chr8:87528000-87551400	Weak transcription	Right Ventricle	heart
49	chr8:87528000-87563800	Weak transcription	Hela-S3	cervix
50	chr8:87528000-87573600	Weak transcription	Stomach Mucosa	stomach

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