Variant report

Variant	rs4454364
Chromosome Location	chr9:86320041-86320042
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	CEBPB	chr9:86320041-86320386	IMR90	lung:	n/a	chr9:86320211-86320222
2	CEBPB	chr9:86320025-86320393	Hela-S3	cervix:	n/a	chr9:86320211-86320222
3	ZNF384	chr9:86319759-86320329	K562	blood:	n/a	n/a
4	ZNF384	chr9:86319701-86321305	GM12878	blood:	n/a	n/a
5	CEBPB	chr9:86320030-86320402	HepG2	liver:	n/a	chr9:86320211-86320222
6	JUND	chr9:86320015-86320221	K562	blood:	n/a	n/a
7	EP300	chr9:86319842-86320117	K562	blood:	n/a	n/a
8	CEBPB	chr9:86320025-86320405	HepG2	liver:	n/a	chr9:86320211-86320222
9	CEBPB	chr9:86319997-86320402	MCF-7	breast:	n/a	chr9:86320211-86320222
10	CEBPB	chr9:86320026-86320321	H1-hESC	embryonic stem cell:	n/a	chr9:86320211-86320222
11	SETDB1	chr9:86319844-86320221	U2OS	brain:	n/a	n/a
12	CEBPB	chr9:86319951-86320401	K562	blood:	n/a	chr9:86320211-86320222
13	CEBPB	chr9:86320016-86320308	HepG2	liver:	n/a	chr9:86320211-86320222
14	CEBPB	chr9:86319946-86320379	K562	blood:	n/a	chr9:86320211-86320222

No.	Distal block	Cell Line	Cell type
1	chr9:85832727..85836639-chr9:86319596..86323973,3	MCF-7	breast:
2	chr9:86319810..86324349-chr9:86592631..86598226,6	K562	blood:
3	chr9:86310182..86311687-chr9:86319047..86320880,2	K562	blood:
4	chr9:85806373..85808943-chr9:86317135..86320093,2	K562	blood:

Variant related genes	Relation type
ENSG00000254473	TF binding region
ENSG00000229109	Chromatin interaction
ENSG00000178966	Chromatin interaction
ENSG00000165119	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10115799	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs10119344	0.85[CHB][hapmap];0.80[ASN][1000 genomes]
rs10125432	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs1035274	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs1044175	0.85[CHB][hapmap]
rs10512136	0.95[CEU][hapmap];0.86[CHB][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes]
rs10512137	0.95[CEU][hapmap];0.86[CHB][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1056073	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10746717	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10746718	0.85[CHB][hapmap]
rs10746719	0.84[CHB][hapmap];0.82[ASN][1000 genomes]
rs10746720	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs10746721	0.85[CHB][hapmap];0.80[ASN][1000 genomes]
rs10780616	0.87[AMR][1000 genomes]
rs10780617	0.88[AMR][1000 genomes]
rs10780618	0.95[CEU][hapmap];0.86[AMR][1000 genomes]
rs10780619	0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs10780620	0.87[AMR][1000 genomes]
rs10780621	0.85[CHB][hapmap]
rs10780622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10780623	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10780624	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10780625	1.00[CEU][hapmap];0.86[CHB][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10868035	0.95[CEU][hapmap];0.86[CHB][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10868036	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10868037	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10868038	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10868040	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs10868042	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10868043	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10868044	0.84[CHB][hapmap];0.82[ASN][1000 genomes]
rs10868045	0.85[CHB][hapmap]
rs11140198	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11140202	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11140209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140212	0.95[CEU][hapmap];0.86[CHB][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11140221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11140223	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11791175	0.85[CHB][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12235741	0.83[AMR][1000 genomes]
rs1333861	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1333862	0.95[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1333863	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs1333865	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs1413293	0.85[CHB][hapmap]
rs1537502	0.95[CEU][hapmap];0.86[CHB][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes]
rs1537503	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1572135	0.85[CHB][hapmap]
rs17080575	0.83[AMR][1000 genomes]
rs1889260	0.85[CHB][hapmap]
rs1961941	0.95[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1968216	0.82[ASN][1000 genomes]
rs2042042	0.82[ASN][1000 genomes]
rs2058912	0.85[CHB][hapmap]
rs2282220	0.95[CEU][hapmap];0.81[CHB][hapmap];0.81[AMR][1000 genomes]
rs2542776	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs2542803	0.82[ASN][1000 genomes]
rs2780969	0.85[CHB][hapmap]
rs2780972	0.85[CHB][hapmap]
rs2780995	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs2781003	0.85[CHB][hapmap]
rs2811909	0.85[CHB][hapmap]
rs2811912	0.85[CHB][hapmap]
rs2811921	0.82[YRI][hapmap]
rs2811923	0.85[CHB][hapmap]
rs2811926	0.85[CHB][hapmap]
rs2811927	0.91[CHB][hapmap]
rs2811928	0.85[CHB][hapmap]
rs2811929	0.85[CHB][hapmap]
rs2811930	0.85[CHB][hapmap]
rs2811931	0.83[CHB][hapmap]
rs3750409	0.94[CEU][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs3750410	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3814505	0.95[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3814507	0.83[AMR][1000 genomes]
rs4146741	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs4242623	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs4877790	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4877791	0.95[CEU][hapmap];0.86[CHB][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4877793	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4877794	0.94[CEU][hapmap];0.86[CHB][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4877796	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4877797	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4877798	0.82[ASN][1000 genomes]
rs4877799	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]
rs4877800	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6559737	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs6559739	0.80[ASN][1000 genomes]
rs7023082	0.85[CHB][hapmap];0.80[ASN][1000 genomes]
rs7039019	0.85[CHB][hapmap];0.80[ASN][1000 genomes]
rs7046388	0.87[AMR][1000 genomes]
rs72618136	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7850944	0.82[ASN][1000 genomes]
rs7860614	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7863266	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7865296	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs7866234	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7871055	0.95[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7874980	0.85[CHB][hapmap]
rs868917	0.95[CEU][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs944946	0.82[ASN][1000 genomes]
rs961807	0.85[CHB][hapmap];0.82[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4454364	RP11-522I20.3	cis	Whole Blood	GTEx
rs4454364	RP11-522I20.3	cis	Muscle Skeletal	GTEx

Chromatin state (count:112 , 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	chr9:86296000-86320800	Weak transcription	Fetal Brain Female	brain
4	chr9:86297600-86321200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr9:86298000-86320400	Weak transcription	Fetal Intestine Large	intestine
6	chr9:86298600-86320400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr9:86298800-86320800	Weak transcription	Fetal Thymus	thymus
8	chr9:86300400-86320400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr9:86300600-86320400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr9:86301000-86320800	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr9:86304400-86320800	Weak transcription	Brain Anterior Caudate	brain
12	chr9:86307600-86320400	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr9:86310400-86320600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr9:86311200-86320800	Weak transcription	Fetal Lung	lung
15	chr9:86311800-86321000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr9:86312800-86320800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr9:86313200-86320800	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr9:86313600-86321000	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr9:86314400-86320800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr9:86314600-86320200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr9:86314600-86321400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr9:86314600-86321400	Weak transcription	Fetal Muscle Trunk	muscle
23	chr9:86314600-86321400	Weak transcription	Gastric	stomach
24	chr9:86314600-86321800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr9:86315000-86320400	Weak transcription	Fetal Heart	heart
26	chr9:86315000-86320600	Weak transcription	Stomach Mucosa	stomach
27	chr9:86315200-86321400	Weak transcription	Aorta	Aorta
28	chr9:86315600-86320400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr9:86315800-86320800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr9:86315800-86320800	Weak transcription	Brain Hippocampus Middle	brain
31	chr9:86316000-86320200	Weak transcription	Right Ventricle	heart
32	chr9:86316000-86320400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr9:86316000-86320600	Weak transcription	Brain Substantia Nigra	brain
34	chr9:86316000-86321400	Weak transcription	Pancreas	Pancrea
35	chr9:86316000-86321800	Weak transcription	Lung	lung
36	chr9:86316600-86320400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr9:86316800-86320400	Weak transcription	Duodenum Mucosa	Duodenum
38	chr9:86317000-86320400	Weak transcription	Adipose Nuclei	Adipose
39	chr9:86317000-86320600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr9:86317000-86320800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr9:86317000-86321000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr9:86317200-86320200	Weak transcription	Primary B cells from peripheral blood	blood
43	chr9:86317200-86320200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr9:86317200-86320400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr9:86317200-86320600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr9:86317200-86320600	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr9:86317200-86320600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr9:86317200-86320600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr9:86317200-86320600	Weak transcription	Brain Angular Gyrus	brain
50	chr9:86317200-86320600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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