Variant report

Variant	rs12605638
Chromosome Location	chr18:12993543-12993544
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr18:12993440-12993590	GM12866	blood:	n/a	n/a
2	WRNIP1	chr18:12993104-12993679	GM12878	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr18:12701267..12703413-chr18:12991110..12994892,3	K562	blood:
2	chr18:12989490..12992525-chr18:12992706..12997077,5	MCF-7	breast:
3	chr18:12945719..12950670-chr18:12989123..12995651,19	K562	blood:
4	chr18:12944429..12952802-chr18:12987284..12998193,21	K562	blood:
5	chr18:12991897..12993724-chr18:13008945..13010565,2	K562	blood:
6	chr18:12991467..12993717-chr18:13539738..13542100,2	MCF-7	breast:
7	chr18:12990627..12994399-chr18:13026748..13030425,3	K562	blood:
8	chr18:12536634..12538194-chr18:12991456..12994159,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000266969	TF binding region
ENSG00000266969	Chromatin interaction
ENSG00000101639	Chromatin interaction
ENSG00000101624	Chromatin interaction
ENSG00000085415	Chromatin interaction
ENSG00000128789	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 13 )

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

rs_ID	r²[population]
rs10221326	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10221384	0.85[EUR][1000 genomes]
rs11080620	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11663049	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12954256	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12955780	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1474043	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1786263	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1786270	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1786279	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1787000	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1787003	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1787004	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1787008	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1973779	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28619103	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28641764	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2902856	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35790309	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3809912	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs472702	0.84[EUR][1000 genomes]
rs472992	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs473580	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs474337	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs475139	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs478006	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs478399	0.84[EUR][1000 genomes]
rs482360	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs482577	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs490853	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs491349	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs492723	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs498685	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4995995	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs518145	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs527839	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs529620	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs547084	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs554719	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs554854	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs556371	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs556536	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs557846	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs562151	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs565832	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs567031	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs569453	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs576963	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs578208	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6505775	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6505776	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6505777	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6505780	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs692833	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs692964	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71353243	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7226616	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7229870	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7233600	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7233814	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7234094	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7234960	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7236162	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7236764	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7237236	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7243660	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8088313	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8089123	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8097038	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8097125	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9783859	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9783903	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9948139	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9948681	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9949589	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9951698	0.85[AMR][1000 genomes]
rs9952698	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9958369	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9961669	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9964466	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9965977	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv1062413	chr18:12988947-13039941	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv543657	chr18:12988947-13039941	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs12605638	CEP192	cis	Stomach	GTEx
rs12605638	CEP192	cis	Artery Tibial	GTEx
rs12605638	CEP192	cis	Thyroid	GTEx
rs12605638	CEP192	cis	lung	GTEx
rs12605638	CEP192	cis	Nerve Tibial	GTEx
rs12605638	CEP192	cis	Whole Blood	GTEx
rs12605638	CEP192	Cis_1M	lymphoblastoid	RTeQTL
rs12605638	CEP192	cis	Esophagus Mucosa	GTEx
rs12605638	CEP192	cis	Skin Sun Exposed Lower leg	GTEx
rs12605638	CEP192	cis	Artery Aorta	GTEx
rs12605638	CEP192	cis	multi-tissue	Pritchard
rs12605638	CEP192	cis	Adipose Subcutaneous	GTEx
rs12605638	CEP192	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12990800-12994800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr18:12992000-12993600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr18:12992000-13000600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr18:12992000-13004400	Weak transcription	Esophagus	oesophagus
5	chr18:12992200-12993600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr18:12992200-12993600	Enhancers	Fetal Brain Male	brain
7	chr18:12992200-13004800	Weak transcription	Aorta	Aorta
8	chr18:12992400-12993800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr18:12992400-12993800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr18:12992400-12993800	Enhancers	Ovary	ovary
11	chr18:12992400-12993800	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr18:12992400-12994200	Enhancers	Primary B cells from peripheral blood	blood
13	chr18:12992400-12994600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr18:12992400-13000400	Weak transcription	Fetal Muscle Trunk	muscle
15	chr18:12992400-13000600	Weak transcription	Placenta	Placenta
16	chr18:12992400-13004400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr18:12992600-12993600	Enhancers	Fetal Intestine Small	intestine
18	chr18:12992600-12993800	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr18:12992600-12993800	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr18:12992600-12993800	Enhancers	Primary T cells fromperipheralblood	blood
21	chr18:12992600-12993800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr18:12992600-12993800	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr18:12992600-12993800	Enhancers	Right Ventricle	heart
24	chr18:12992600-12993800	Enhancers	Small Intestine	intestine
25	chr18:12992600-12993800	Flanking Active TSS	Hela-S3	cervix
26	chr18:12992600-12994000	Enhancers	Colon Smooth Muscle	Colon
27	chr18:12992600-12994600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr18:12992600-12994800	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr18:12992600-12994800	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr18:12992600-13000400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr18:12992600-13031200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr18:12992800-12993600	Enhancers	Primary B cells from cord blood	blood
33	chr18:12992800-12993600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr18:12992800-12993600	Enhancers	Fetal Heart	heart
35	chr18:12992800-12993600	Enhancers	Right Atrium	heart
36	chr18:12992800-12993800	Enhancers	Primary T cells from cord blood	blood
37	chr18:12992800-12993800	Enhancers	Fetal Thymus	thymus
38	chr18:12992800-12993800	Enhancers	Left Ventricle	heart
39	chr18:12992800-12993800	Enhancers	Rectal Smooth Muscle	rectum
40	chr18:12992800-12994400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr18:12992800-12995000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr18:12992800-12996000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr18:12992800-12996400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr18:12992800-12997600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr18:12992800-13004000	Weak transcription	Stomach Smooth Muscle	stomach
46	chr18:12992800-13008800	Weak transcription	Colonic Mucosa	Colon
47	chr18:12992800-13009200	Weak transcription	Brain Cingulate Gyrus	brain
48	chr18:12992800-13013200	Weak transcription	Fetal Kidney	kidney
49	chr18:12992800-13016000	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr18:12993000-12993600	Enhancers	Lung	lung

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