Variant report

Variant	rs1333862
Chromosome Location	chr9:86324250-86324251
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	POLR2A	chr9:86324080-86324298	HepG2	liver:	n/a	n/a
2	POLR2A	chr9:86322001-86324319	HepG2	liver:	n/a	n/a
3	POLR2A	chr9:86322622-86324469	K562	blood:	n/a	n/a
4	WRNIP1	chr9:86322689-86324256	GM12878	blood:	n/a	n/a
5	POLR2A	chr9:86321700-86324311	H1-hESC	embryonic stem cell:	n/a	n/a
6	JUND	chr9:86322061-86324304	SK-N-SH	brain:	n/a	chr9:86322616-86322626 chr9:86323857-86323866 chr9:86322616-86322626 chr9:86322617-86322625 chr9:86323146-86323155

No.	Distal block	Cell Line	Cell type
1	chr9:86298986..86303456-chr9:86320609..86324425,4	MCF-7	breast:
2	chr9:86319810..86324349-chr9:86592631..86598226,6	K562	blood:
3	chr9:86321469..86324662-chr9:86431245..86433854,3	MCF-7	breast:
4	chr9:80644449..80646704-chr9:86322574..86325176,2	MCF-7	breast:
5	chr17:56737660..56739734-chr9:86322211..86324865,2	MCF-7	breast:
6	chr9:86321248..86324502-chr9:86534491..86537588,5	MCF-7	breast:
7	chr9:86320289..86324589-chr9:86593742..86599530,6	K562	blood:
8	chr9:86236280..86241962-chr9:86320992..86325340,9	MCF-7	breast:

Variant related genes	Relation type
UBQLN1	TF binding region
ENSG00000148057	Chromatin interaction
ENSG00000156052	Chromatin interaction
ENSG00000178966	Chromatin interaction
ENSG00000135018	Chromatin interaction
ENSG00000165113	Chromatin interaction
ENSG00000165119	Chromatin interaction
ENSG00000165115	Chromatin interaction
ENSG00000266826	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10512136	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10512137	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1056073	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10746717	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10780616	0.87[AMR][1000 genomes]
rs10780617	0.88[AMR][1000 genomes]
rs10780618	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes]
rs10780619	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs10780620	0.87[AMR][1000 genomes]
rs10780622	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10780623	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10780624	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10780625	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10868035	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10868036	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10868037	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10868038	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10868042	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10868043	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11140198	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11140202	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11140209	0.95[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11140212	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11140221	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11140223	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11791175	1.00[CHB][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12235741	0.83[AMR][1000 genomes]
rs1333861	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1537502	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1537503	0.95[CEU][hapmap];0.94[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs17080575	0.87[MEX][hapmap];0.83[AMR][1000 genomes]
rs1961941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2282220	1.00[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2811921	0.93[CHB][hapmap];0.82[CHD][hapmap];0.82[YRI][hapmap]
rs2811927	0.83[CHB][hapmap]
rs3750409	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs3750410	0.95[CEU][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs3814505	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3814507	0.88[MEX][hapmap];0.83[AMR][1000 genomes]
rs4146740	0.80[EUR][1000 genomes]
rs4454364	0.95[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4877790	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4877791	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4877793	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4877794	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4877796	1.00[ASW][hapmap];0.95[CEU][hapmap];0.94[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4877797	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4877799	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]
rs4877800	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7046388	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72618136	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7860614	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7863266	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7866234	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7871055	0.90[CEU][hapmap];0.84[LWK][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs868917	1.00[CEU][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
rs1333862	RP11-522I20.3	cis	Muscle Skeletal	GTEx
rs1333862	RP11-522I20.3	cis	Whole Blood	GTEx
rs1333862	UBQLN1	cis	lymphoblastoid	seeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86323200-86324400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr9:86323800-86324600	Enhancers	Fetal Heart	heart
3	chr9:86323800-86324600	Enhancers	Sigmoid Colon	Sigmoid Colon
4	chr9:86323800-86325800	Weak transcription	Psoas Muscle	Psoas
5	chr9:86324000-86324400	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr9:86324000-86324400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr9:86324000-86324400	Enhancers	HepG2	liver
8	chr9:86324000-86324600	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr9:86324000-86324600	Enhancers	Pancreas	Pancrea
10	chr9:86324000-86324600	Enhancers	NHDF-Ad	bronchial
11	chr9:86324200-86324400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr9:86324200-86324400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr9:86324200-86324400	Enhancers	Adipose Nuclei	Adipose
14	chr9:86324200-86324400	Enhancers	Liver	Liver
15	chr9:86324200-86324400	Enhancers	Fetal Kidney	kidney
16	chr9:86324200-86324400	Enhancers	Pancreatic Islets	Pancreatic Islet
17	chr9:86324200-86324400	Enhancers	NHEK	skin
18	chr9:86324200-86324600	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr9:86324200-86324600	Enhancers	Primary hematopoietic stem cells	blood
20	chr9:86324200-86324600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr9:86324200-86324600	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr9:86324200-86324600	Enhancers	Dnd41	blood
23	chr9:86324200-86324600	Enhancers	K562	blood
24	chr9:86324200-86326000	Weak transcription	Primary B cells from cord blood	blood
25	chr9:86324200-86327600	Weak transcription	Brain Cingulate Gyrus	brain
26	chr9:86324200-86327600	Weak transcription	Brain Substantia Nigra	brain
27	chr9:86324200-86327800	Weak transcription	Brain Anterior Caudate	brain
28	chr9:86324200-86327800	Weak transcription	Brain Hippocampus Middle	brain
29	chr9:86324200-86328200	Weak transcription	Fetal Intestine Small	intestine
30	chr9:86324200-86328800	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr9:86324200-86328800	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr9:86324200-86329000	Weak transcription	Fetal Muscle Leg	muscle
33	chr9:86324200-86329200	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr9:86324200-86329200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr9:86324200-86330000	Weak transcription	Primary T cells from cord blood	blood
36	chr9:86324200-86330400	Weak transcription	HSMMtube	muscle
37	chr9:86324200-86331000	Weak transcription	Brain Angular Gyrus	brain
38	chr9:86324200-86331800	Weak transcription	Skeletal Muscle Male	skeletal muscle

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