Variant report

Variant	rs6505777
Chromosome Location	chr18:13008369-13008370
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	chr18:13007857-13008375	K562	blood:	n/a	n/a
2	CTCF	chr18:13008220-13008370	GM06990	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:12989546..12991386-chr18:13006007..13008502,2	K562	blood:
2	chr18:12946237..12948654-chr18:13006557..13008669,3	K562	blood:

Variant related genes	Relation type
CEP192	TF binding region
ENSG00000085415	Chromatin interaction
ENSG00000266969	Chromatin interaction
ENSG00000101639	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10221326	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10221384	0.86[EUR][1000 genomes]
rs11080620	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11663049	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12605638	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12954256	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12955780	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1474043	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1786263	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1786270	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1786279	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1787000	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1787003	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1787004	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1787008	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1973779	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28619103	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28641764	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2902856	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35790309	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3809912	0.81[AMR][1000 genomes]
rs472702	0.85[EUR][1000 genomes]
rs472992	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs473580	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs474337	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs475139	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs478006	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs478399	0.85[EUR][1000 genomes]
rs482360	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs482577	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs490853	0.98[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs491349	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs492723	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs498685	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4995995	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs518145	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs527839	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs529620	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs547084	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs554719	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs554854	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs556371	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs556536	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs557846	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs562151	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs565832	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs567031	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs569453	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs576963	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs578208	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6505775	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6505776	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6505780	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs692833	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs692964	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71353243	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7226616	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7229870	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7233600	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7233814	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7234094	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7234960	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7236162	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7236764	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7237236	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7243660	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8088313	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8089123	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8097038	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8097125	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9783859	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9783903	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9948139	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9948681	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9949589	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9951698	0.83[AMR][1000 genomes]
rs9952698	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9958369	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9961669	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9964466	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[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
rs6505777	CEP192	Cis_1M	lymphoblastoid	RTeQTL
rs6505777	CEP192	cis	Nerve Tibial	GTEx
rs6505777	CEP192	cis	Artery Aorta	GTEx
rs6505777	CEP192	cis	Whole Blood	GTEx
rs6505777	CEP192	cis	multi-tissue	Pritchard
rs6505777	CEP192	cis	Adipose Subcutaneous	GTEx
rs6505777	CEP192	cis	lung	GTEx
rs6505777	CEP192	cis	Artery Tibial	GTEx
rs6505777	CEP192	cis	Thyroid	GTEx
rs6505777	CEP192	cis	Skin Sun Exposed Lower leg	GTEx
rs6505777	CEP192	cis	Esophagus Muscularis	GTEx
rs6505777	CEP192	cis	Esophagus Mucosa	GTEx
rs6505777	CEP192	cis	Stomach	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12992600-13031200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr18:12992800-13008800	Weak transcription	Colonic Mucosa	Colon
3	chr18:12992800-13009200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr18:12992800-13013200	Weak transcription	Fetal Kidney	kidney
5	chr18:12992800-13016000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr18:12993000-13023800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr18:12993200-13008400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr18:12993200-13008400	Weak transcription	Osteobl	bone
9	chr18:12993200-13008800	Weak transcription	NHLF	lung
10	chr18:12993400-13017800	Weak transcription	Stomach Mucosa	stomach
11	chr18:12993600-13011800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr18:12993600-13011800	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr18:12993800-13008400	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr18:12993800-13008400	Weak transcription	Psoas Muscle	Psoas
15	chr18:12993800-13008400	Weak transcription	HMEC	breast
16	chr18:12993800-13008800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr18:12993800-13009200	Weak transcription	NHDF-Ad	bronchial
18	chr18:12995000-13011400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr18:12995200-13042000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr18:12997000-13008600	Weak transcription	Brain Anterior Caudate	brain
21	chr18:12997000-13008800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr18:12997200-13011200	Weak transcription	Right Ventricle	heart
23	chr18:12997200-13013200	Weak transcription	Small Intestine	intestine
24	chr18:12997400-13008800	Weak transcription	Pancreas	Pancrea
25	chr18:12997400-13015000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr18:12998400-13041600	Strong transcription	Dnd41	blood
27	chr18:12998600-13008600	Weak transcription	Colon Smooth Muscle	Colon
28	chr18:12999000-13008800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr18:12999000-13011800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr18:12999200-13039000	Strong transcription	Fetal Thymus	thymus
31	chr18:12999400-13020800	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr18:12999400-13021800	Strong transcription	Primary T cells from cord blood	blood
33	chr18:12999600-13017200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr18:12999600-13018800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr18:13000200-13011200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr18:13000400-13034000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr18:13001600-13008400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr18:13001600-13008400	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr18:13001600-13008400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr18:13001600-13008600	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr18:13001800-13008400	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr18:13002000-13008400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr18:13002200-13008400	Weak transcription	HSMM	muscle
44	chr18:13002800-13008600	Weak transcription	Placenta	Placenta
45	chr18:13002800-13021200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr18:13003000-13011400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr18:13003200-13011200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr18:13003400-13016800	Strong transcription	Thymus	Thymus
49	chr18:13003800-13008800	Weak transcription	A549	lung
50	chr18:13004000-13008600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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