Variant report

Variant	rs6505775
Chromosome Location	chr18:12978183-12978184
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:12977170..12978681-chr18:12990221..12993190,2	MCF-7	breast:
2	chr18:12969942..12972168-chr18:12978134..12980197,2	K562	blood:
3	chr18:12977438..12979296-chr18:12990126..12991644,2	K562	blood:
4	chr18:12977796..12979633-chr18:12990126..12992980,2	K562	blood:

Variant related genes	Relation type
ENSG00000266969	Chromatin interaction
ENSG00000085415	Chromatin interaction
ENSG00000101639	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 13 )

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

rs_ID	r²[population]
rs10221326	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10221384	0.81[EUR][1000 genomes]
rs11080620	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11663049	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12605638	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12954256	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12955780	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1474043	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1786263	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1786270	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1786279	0.81[EUR][1000 genomes]
rs1787000	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1787003	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1787004	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1787008	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1973779	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28619103	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28641764	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2902856	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35790309	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3809912	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs472702	0.80[EUR][1000 genomes]
rs472992	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs473580	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs474337	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs475139	0.82[EUR][1000 genomes]
rs478006	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs478399	0.80[EUR][1000 genomes]
rs482360	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs482577	0.80[EUR][1000 genomes]
rs490853	0.92[AMR][1000 genomes]
rs492723	0.81[EUR][1000 genomes]
rs498685	0.84[EUR][1000 genomes]
rs4995995	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs518145	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs527839	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs529620	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs547084	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs554719	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs554854	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs556371	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs556536	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs557846	0.82[EUR][1000 genomes]
rs562151	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs565832	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs567031	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs569453	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs576963	0.81[EUR][1000 genomes]
rs578208	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6505776	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6505777	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6505780	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs692833	0.81[EUR][1000 genomes]
rs692964	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71353243	0.82[EUR][1000 genomes]
rs7226616	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7229870	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7233600	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7233814	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7234094	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7234960	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7236162	0.80[EUR][1000 genomes]
rs7236764	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7237236	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7243660	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8088313	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8089123	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8097038	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8097125	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9783859	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9783903	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9948139	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9948681	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9949589	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9951698	0.88[AMR][1000 genomes]
rs9952698	0.82[EUR][1000 genomes]
rs9958369	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9961669	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9964466	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9965977	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs6505775	CEP192	cis	Skin Sun Exposed Lower leg	GTEx
rs6505775	CEP192	cis	lung	GTEx
rs6505775	CEP192	Cis_1M	lymphoblastoid	RTeQTL
rs6505775	CEP192	cis	Nerve Tibial	GTEx
rs6505775	CEP192	cis	Esophagus Muscularis	GTEx
rs6505775	CEP192	cis	Thyroid	GTEx
rs6505775	CEP192	cis	Esophagus Mucosa	GTEx
rs6505775	CEP192	cis	Adipose Subcutaneous	GTEx
rs6505775	CEP192	cis	Whole Blood	GTEx
rs6505775	CEP192	cis	Stomach	GTEx
rs6505775	CEP192	cis	Artery Aorta	GTEx
rs6505775	CEP192	cis	multi-tissue	Pritchard
rs6505775	CEP192	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12948800-12989000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr18:12949200-12989400	Weak transcription	Psoas Muscle	Psoas
3	chr18:12950000-12990200	Weak transcription	Fetal Brain Male	brain
4	chr18:12951400-12990200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr18:12951600-12988200	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr18:12951800-12978400	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr18:12953200-12979000	Strong transcription	Fetal Thymus	thymus
8	chr18:12957400-12978400	Strong transcription	Dnd41	blood
9	chr18:12959000-12990200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr18:12959200-12978200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr18:12961000-12978400	Strong transcription	Fetal Intestine Small	intestine
12	chr18:12963200-12978600	Strong transcription	Fetal Intestine Large	intestine
13	chr18:12963600-12978600	Strong transcription	Fetal Stomach	stomach
14	chr18:12968600-12983000	Weak transcription	HUVEC	blood vessel
15	chr18:12969800-12979000	Strong transcription	Primary B cells from cord blood	blood
16	chr18:12969800-12979000	Strong transcription	Osteobl	bone
17	chr18:12970000-12979000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr18:12970000-12979000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr18:12970200-12978200	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr18:12970200-12978600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr18:12970200-12978800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr18:12970200-12978800	Strong transcription	Liver	Liver
23	chr18:12970200-12979000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr18:12970200-12979000	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr18:12970400-12978200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr18:12970400-12978600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr18:12970400-12979000	Strong transcription	Primary T cells from cord blood	blood
28	chr18:12970400-12979000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr18:12970400-12979000	Strong transcription	Fetal Muscle Trunk	muscle
30	chr18:12970400-12979200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr18:12970400-12979200	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr18:12970600-12978400	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr18:12970600-12978400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr18:12970600-12978800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr18:12970600-12979000	Strong transcription	H1 Cell Line	embryonic stem cell
36	chr18:12970600-12979000	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr18:12970600-12979000	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr18:12970800-12978400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr18:12970800-12978800	Strong transcription	Fetal Muscle Leg	muscle
40	chr18:12970800-12978800	Strong transcription	Thymus	Thymus
41	chr18:12970800-12979000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr18:12970800-12979000	Strong transcription	Duodenum Mucosa	Duodenum
43	chr18:12970800-12979200	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr18:12971000-12978800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr18:12971000-12979000	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr18:12971000-12979000	Strong transcription	Primary B cells from peripheral blood	blood
47	chr18:12971400-12978200	Strong transcription	Placenta	Placenta
48	chr18:12971600-12979000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr18:12971600-12979000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr18:12972800-12990000	Weak transcription	Brain Substantia Nigra	brain

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