Variant report

Variant	rs554854
Chromosome Location	chr18:13101168-13101169
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	chr18:13101048-13101215	K562	blood:	n/a	n/a
2	POLR2A	chr18:13100576-13101189	K562	blood:	n/a	n/a
3	POLR2A	chr18:13100106-13101516	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:13099273..13102130-chr18:13123064..13124628,2	MCF-7	breast:

Variant related genes	Relation type
CEP192	TF binding region

Extended variants
information (count: 88 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10221326	0.92[CHB][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10221384	0.85[CEU][hapmap]
rs11080620	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11663049	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12605638	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12954256	0.89[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12955780	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1474043	0.89[CEU][hapmap];0.87[CHB][hapmap];0.85[AMR][1000 genomes]
rs1786263	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1786270	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1786279	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1787000	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1787003	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1787004	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1787008	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1973779	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28619103	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28641764	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2902856	0.82[CEU][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35790309	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3809912	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs472702	0.89[CEU][hapmap];0.81[AMR][1000 genomes]
rs472992	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs473580	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs474337	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs475139	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs478006	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs478399	0.81[AMR][1000 genomes]
rs482360	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs482577	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs490853	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs491349	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs492723	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs498685	0.89[CEU][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4995995	0.85[AMR][1000 genomes]
rs518145	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs527839	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs529620	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs547084	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs554719	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs556371	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs556536	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs557846	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs562151	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs565832	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs567031	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs569453	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs570505	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs576963	0.96[CEU][hapmap];0.86[CHB][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs578208	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6505775	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6505776	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6505777	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6505780	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs692833	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs692964	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71353243	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7226616	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7229870	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7233600	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7233814	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7234094	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7234960	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7236162	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7236764	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7237236	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7241536	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7243660	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8088313	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8089123	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs8097038	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8097125	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9783859	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9783903	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9948139	0.85[AMR][1000 genomes]
rs9949589	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9949682	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9952698	0.81[AMR][1000 genomes]
rs9958369	0.86[AMR][1000 genomes]
rs9961669	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9964466	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
3	nsv1057083	chr18:12916779-13207538	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv576524	chr18:12918318-13183609	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv1056593	chr18:12926314-13183383	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	nsv1064364	chr18:12926314-13207686	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	nsv833591	chr18:13093777-13253748	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs554854	CEP192	cis	Temporal Cortex	GTEx
rs554854	CEP192	cis	Esophagus Mucosa	GTEx
rs554854	CEP192	cis	Artery Tibial	GTEx
rs554854	CEP192	cis	multi-tissue	Pritchard
rs554854	CEP192	cis	Nerve Tibial	GTEx
rs554854	CEP192	cis	lung	GTEx
rs554854	CEP192	Cis_1M	lymphoblastoid	RTeQTL
rs554854	CEP192	cis	Adipose Subcutaneous	GTEx
rs554854	CEP192	cis	Artery Aorta	GTEx
rs554854	CEP192	cis	Stomach	GTEx
rs554854	CEP192	cis	Esophagus Muscularis	GTEx
rs554854	CEP192	cis	Skin Sun Exposed Lower leg	GTEx
rs554854	CEP192	cis	Whole Blood	GTEx
rs554854	CEP192	cis	Brain Pons	GTEx
rs554854	CEP192	cis	Thyroid	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:13018600-13117400	Weak transcription	Stomach Mucosa	stomach
2	chr18:13075400-13105400	Weak transcription	Psoas Muscle	Psoas
3	chr18:13086000-13109400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr18:13086400-13128000	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr18:13089400-13122200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr18:13090600-13109200	Strong transcription	Fetal Muscle Trunk	muscle
7	chr18:13091200-13110800	Weak transcription	Right Atrium	heart
8	chr18:13092800-13106800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr18:13093000-13109400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr18:13093000-13111200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr18:13093400-13111200	Strong transcription	Fetal Muscle Leg	muscle
12	chr18:13095400-13109600	Strong transcription	H1 Cell Line	embryonic stem cell
13	chr18:13096800-13105400	Weak transcription	Fetal Brain Male	brain
14	chr18:13097000-13101200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr18:13097000-13101200	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr18:13097200-13101400	Weak transcription	Pancreas	Pancrea
17	chr18:13097200-13103800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr18:13097200-13105000	Weak transcription	NHDF-Ad	bronchial
19	chr18:13097200-13118800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr18:13097400-13101400	Weak transcription	Brain Substantia Nigra	brain
21	chr18:13097400-13102400	Weak transcription	HSMMtube	muscle
22	chr18:13097400-13102600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr18:13097400-13105000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr18:13097400-13105000	Weak transcription	Fetal Kidney	kidney
25	chr18:13097600-13101200	Weak transcription	HepG2	liver
26	chr18:13097600-13101600	Weak transcription	Aorta	Aorta
27	chr18:13097600-13102400	Weak transcription	Colon Smooth Muscle	Colon
28	chr18:13097600-13102800	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr18:13097600-13103600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr18:13097600-13104200	Weak transcription	Small Intestine	intestine
31	chr18:13097600-13111600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr18:13098400-13102400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr18:13098400-13109400	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr18:13098600-13106400	Strong transcription	Thymus	Thymus
35	chr18:13098600-13108200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr18:13098800-13106600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr18:13098800-13107800	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr18:13098800-13121200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr18:13099000-13109600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr18:13099200-13106200	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr18:13099200-13107200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr18:13099200-13108000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr18:13099200-13108000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr18:13099200-13108200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr18:13099200-13108600	Strong transcription	Primary hematopoietic stem cells	blood
46	chr18:13099200-13109200	Strong transcription	Primary B cells from peripheral blood	blood
47	chr18:13099200-13109200	Strong transcription	Brain Anterior Caudate	brain
48	chr18:13099200-13109200	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr18:13099200-13109200	Strong transcription	A549	lung
50	chr18:13099200-13109400	Strong transcription	Primary T helper cells fromperipheralblood	blood

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