Variant report

Variant	rs4877799
Chromosome Location	chr9:86321317-86321318
allele	A/G
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	POLR2A	chr9:86321046-86322390	K562	blood:	n/a	n/a
2	EP300	chr9:86321303-86321683	K562	blood:	n/a	chr9:86321305-86321319
3	CUX1	chr9:86321026-86321411	K562	blood:	n/a	n/a
4	EBF1	chr9:86321185-86322443	GM12878	blood:	n/a	chr9:86321427-86321436 chr9:86321426-86321437 chr9:86321427-86321436 chr9:86321427-86321437 chr9:86321425-86321438
5	CUX1	chr9:86321224-86321900	GM12878	blood:	n/a	n/a
6	MXI1	chr9:86321118-86323807	IMR90	lung:	n/a	n/a
7	MXI1	chr9:86320903-86324125	SK-N-SH	brain:	n/a	n/a
8	ARID3A	chr9:86321301-86321608	K562	blood:	n/a	chr9:86321579-86321595
9	RCOR1	chr9:86321157-86321947	GM12878	blood:	n/a	n/a
10	MAZ	chr9:86321159-86323782	GM12878	blood:	n/a	chr9:86322881-86322890 chr9:86322045-86322055

No.	Distal block	Cell Line	Cell type
1	chr9:86283424..86286026-chr9:86321121..86323958,3	MCF-7	breast:
2	chr9:85832727..85836639-chr9:86319596..86323973,3	MCF-7	breast:
3	chr9:86263962..86264724-chr9:86321097..86322063,2	MCF-7	breast:
4	chr9:86321176..86323111-chr9:86534764..86537575,5	MCF-7	breast:
5	chr9:86298986..86303456-chr9:86320609..86324425,4	MCF-7	breast:
6	chr9:86319810..86324349-chr9:86592631..86598226,6	K562	blood:
7	chr5:81987635..81988277-chr9:86321159..86321783,2	MCF-7	breast:
8	chr9:86300840..86303166-chr9:86321097..86323645,3	K562	blood:
9	chr9:86321248..86324502-chr9:86534491..86537588,5	MCF-7	breast:
10	chr9:86320289..86324589-chr9:86593742..86599530,6	K562	blood:
11	chr9:86320718..86323719-chr9:86450162..86455199,6	MCF-7	breast:
12	chr9:86236280..86241962-chr9:86320992..86325340,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254473	TF binding region
ENSG00000148057	Chromatin interaction
ENSG00000229109	Chromatin interaction
ENSG00000165115	Chromatin interaction
ENSG00000178966	Chromatin interaction
ENSG00000165119	Chromatin interaction
ENSG00000135018	Chromatin interaction
ENSG00000226877	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10512136	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10512137	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];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1056073	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10746717	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10780616	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10780617	0.87[AMR][1000 genomes]
rs10780618	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes]
rs10780619	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs10780620	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10780622	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10780623	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10780624	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10780625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10868035	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10868036	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10868037	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10868038	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10868042	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10868043	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11140198	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11140202	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11140209	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11140212	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11140221	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140223	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11791175	1.00[CHB][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12235741	0.84[AMR][1000 genomes]
rs1333861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1333862	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1537502	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1537503	0.94[CEU][hapmap];0.86[CHB][hapmap];0.97[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs17080575	0.87[MEX][hapmap];0.84[AMR][1000 genomes]
rs1961941	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2282220	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2811921	0.86[CHB][hapmap];0.82[CHD][hapmap];0.82[YRI][hapmap]
rs3750409	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3750410	0.94[CEU][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs3814505	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3814507	0.88[MEX][hapmap];0.84[AMR][1000 genomes]
rs4146740	0.81[EUR][1000 genomes]
rs4454364	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4877790	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4877791	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];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4877793	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4877794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4877796	1.00[ASW][hapmap];0.94[CEU][hapmap];0.86[CHB][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4877797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4877800	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7046388	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72618136	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7860614	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7863266	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7866234	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7871055	0.89[CEU][hapmap];0.89[LWK][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs868917	1.00[CEU][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];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	nsv893512	chr9:86022215-86323309	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1044639	chr9:86252505-86412041	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv893513	chr9:86298632-86433459	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4877799	RP11-522I20.3	cis	Whole Blood	GTEx
rs4877799	RP11-522I20.3	cis	Muscle Skeletal	GTEx
rs4877799	UBQLN1	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86289000-86321800	Weak transcription	Esophagus	oesophagus
2	chr9:86294000-86321800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr9:86314600-86321400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr9:86314600-86321400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr9:86314600-86321400	Weak transcription	Gastric	stomach
6	chr9:86314600-86321800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr9:86315200-86321400	Weak transcription	Aorta	Aorta
8	chr9:86316000-86321400	Weak transcription	Pancreas	Pancrea
9	chr9:86316000-86321800	Weak transcription	Lung	lung
10	chr9:86317200-86321400	Weak transcription	Left Ventricle	heart
11	chr9:86318000-86324000	Active TSS	GM12878-XiMat	blood
12	chr9:86318200-86321800	Weak transcription	Small Intestine	intestine
13	chr9:86320000-86323400	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr9:86320200-86321400	Enhancers	Primary B cells from peripheral blood	blood
15	chr9:86320200-86321600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
16	chr9:86320200-86322000	Weak transcription	Spleen	Spleen
17	chr9:86320200-86323800	Active TSS	K562	blood
18	chr9:86320400-86321400	Flanking Active TSS	Hela-S3	cervix
19	chr9:86320400-86321600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr9:86320400-86321800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr9:86320400-86322000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr9:86320400-86322000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr9:86320400-86323800	Active TSS	Psoas Muscle	Psoas
24	chr9:86320400-86324000	Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr9:86320600-86321400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr9:86320600-86321400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr9:86320600-86321400	Flanking Active TSS	HUVEC	blood vessel
28	chr9:86320600-86321800	Flanking Active TSS	Primary T cells from cord blood	blood
29	chr9:86320600-86321800	Flanking Active TSS	Primary hematopoietic stem cells	blood
30	chr9:86320600-86321800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
31	chr9:86320600-86321800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr9:86320600-86321800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr9:86320600-86321800	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr9:86320600-86322200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr9:86320600-86324000	Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr9:86320600-86324000	Active TSS	HUES64 Cell Line	embryonic stem cell
37	chr9:86320800-86321400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr9:86320800-86321400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr9:86320800-86321400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
40	chr9:86320800-86321400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
41	chr9:86320800-86321400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr9:86320800-86321400	Weak transcription	Stomach Mucosa	stomach
43	chr9:86320800-86321600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr9:86320800-86321600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
45	chr9:86320800-86321600	Flanking Active TSS	Colon Smooth Muscle	Colon
46	chr9:86320800-86321600	Flanking Active TSS	Fetal Brain Male	brain
47	chr9:86320800-86321600	Flanking Active TSS	Fetal Heart	heart
48	chr9:86320800-86321600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
49	chr9:86320800-86321600	Flanking Active TSS	Rectal Smooth Muscle	rectum
50	chr9:86320800-86321600	Flanking Active TSS	Osteobl	bone

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