Variant report

Variant	rs66808227
Chromosome Location	chr18:12679828-12679829
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	chr18:12678931-12680070	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr18:12678940-12680232	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:12679696..12682391-chr18:12945216..12947910,2	K562	blood:
2	chr18:12375835..12378198-chr18:12677932..12680535,3	K562	blood:
3	chr18:12677577..12680065-chr18:12699898..12703044,3	K562	blood:

Variant related genes	Relation type
CEP76	TF binding region
ENSG00000085415	Chromatin interaction
ENSG00000128789	Chromatin interaction
ENSG00000101624	Chromatin interaction
ENSG00000141385	Chromatin interaction

Extended variants
information (count: 116 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs1062235	0.92[ASN][1000 genomes]
rs1129214	0.92[ASN][1000 genomes]
rs12373207	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12373259	0.91[ASN][1000 genomes]
rs12454322	0.84[EUR][1000 genomes]
rs12455268	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12455295	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12457771	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12458097	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12458895	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12954079	0.92[ASN][1000 genomes]
rs12957555	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12957603	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12957810	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12960623	0.96[ASN][1000 genomes]
rs12960997	0.92[ASN][1000 genomes]
rs12962598	0.92[ASN][1000 genomes]
rs12963505	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12964507	0.91[ASN][1000 genomes]
rs12965733	0.87[ASN][1000 genomes]
rs12965990	0.92[ASN][1000 genomes]
rs12966246	0.86[ASN][1000 genomes]
rs12966367	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12966424	0.92[ASN][1000 genomes]
rs12968771	0.96[ASN][1000 genomes]
rs12969300	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12969446	0.92[ASN][1000 genomes]
rs12969938	0.92[ASN][1000 genomes]
rs12971256	0.87[ASN][1000 genomes]
rs1362709	0.90[ASN][1000 genomes]
rs1549011	0.92[ASN][1000 genomes]
rs1592642	0.87[ASN][1000 genomes]
rs1592643	0.87[ASN][1000 genomes]
rs17616402	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1971702	0.86[ASN][1000 genomes]
rs2011575	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2011579	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2051262	0.91[ASN][1000 genomes]
rs2302768	0.91[ASN][1000 genomes]
rs28820339	0.87[ASN][1000 genomes]
rs28832066	0.92[ASN][1000 genomes]
rs34040888	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34120824	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34277169	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34472716	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34537593	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34632667	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34690304	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34847769	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35322088	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35506854	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35634465	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35699948	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35898717	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3809919	0.91[ASN][1000 genomes]
rs3902981	0.85[ASN][1000 genomes]
rs4296322	0.88[ASN][1000 genomes]
rs45589535	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45596833	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4633785	0.92[ASN][1000 genomes]
rs55870255	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62095975	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62096023	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62096046	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62096048	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6505760	0.87[ASN][1000 genomes]
rs7233175	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7233694	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7507018	0.92[ASN][1000 genomes]
rs8083182	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8083217	0.82[ASN][1000 genomes]
rs8086099	0.87[ASN][1000 genomes]
rs8086265	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8086846	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8097134	0.87[ASN][1000 genomes]
rs9303774	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9303775	0.92[ASN][1000 genomes]
rs9303776	0.89[ASN][1000 genomes]
rs933600	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs948319	0.91[ASN][1000 genomes]
rs963920	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9945140	0.92[ASN][1000 genomes]
rs9945644	0.92[ASN][1000 genomes]
rs9945801	0.92[ASN][1000 genomes]
rs9948844	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9949293	0.92[ASN][1000 genomes]
rs9950365	0.92[ASN][1000 genomes]
rs9951576	0.92[ASN][1000 genomes]
rs9952000	0.92[ASN][1000 genomes]
rs9954112	0.92[ASN][1000 genomes]
rs9955985	0.92[ASN][1000 genomes]
rs9957880	0.91[ASN][1000 genomes]
rs9958100	0.90[ASN][1000 genomes]
rs9958412	0.92[ASN][1000 genomes]
rs9959039	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9959458	0.92[ASN][1000 genomes]
rs9959536	0.91[ASN][1000 genomes]
rs9960555	0.91[ASN][1000 genomes]
rs9961799	0.87[ASN][1000 genomes]
rs9962006	0.92[ASN][1000 genomes]
rs9963809	0.87[ASN][1000 genomes]
rs9964868	0.94[ASN][1000 genomes]
rs9966464	0.90[ASN][1000 genomes]
rs9966490	0.91[ASN][1000 genomes]
rs9966672	0.91[ASN][1000 genomes]
rs9967437	0.92[ASN][1000 genomes]
rs9967553	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	esv3528039	chr18:12396582-12851293	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	esv3528041	chr18:12396641-12851245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv523743	chr18:12474505-12742809	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv1820040	chr18:12635601-12725236	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	esv1817845	chr18:12635601-12733705	Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	esv1821625	chr18:12635601-12733705	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	esv1791969	chr18:12643193-12697711	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs66808227	RP11-861E21.2	cis	Muscle Skeletal	GTEx
rs66808227	SPIRE1	cis	Muscle Skeletal	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12658800-12701800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr18:12659000-12700200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr18:12660000-12692600	Weak transcription	Brain Cingulate Gyrus	brain
4	chr18:12660400-12700800	Weak transcription	Fetal Brain Male	brain
5	chr18:12662800-12701600	Weak transcription	Aorta	Aorta
6	chr18:12665800-12684200	Weak transcription	Pancreas	Pancrea
7	chr18:12667000-12701600	Weak transcription	Gastric	stomach
8	chr18:12668400-12694800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr18:12668600-12685800	Weak transcription	Brain Hippocampus Middle	brain
10	chr18:12669200-12694200	Weak transcription	A549	lung
11	chr18:12669800-12694200	Weak transcription	Hela-S3	cervix
12	chr18:12671600-12680000	Strong transcription	Fetal Intestine Large	intestine
13	chr18:12672200-12701400	Weak transcription	Colonic Mucosa	Colon
14	chr18:12672400-12680200	Strong transcription	HepG2	liver
15	chr18:12672400-12687400	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr18:12672400-12697200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr18:12673200-12701600	Weak transcription	Psoas Muscle	Psoas
18	chr18:12673400-12680200	Strong transcription	Fetal Intestine Small	intestine
19	chr18:12674200-12693800	Weak transcription	NHEK	skin
20	chr18:12674600-12693800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr18:12674600-12701600	Weak transcription	Right Ventricle	heart
22	chr18:12674600-12701600	Weak transcription	Small Intestine	intestine
23	chr18:12674800-12682200	Weak transcription	Fetal Brain Female	brain
24	chr18:12674800-12685000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr18:12674800-12686200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr18:12674800-12700600	Weak transcription	Brain Substantia Nigra	brain
27	chr18:12674800-12701400	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr18:12675000-12694000	Weak transcription	Stomach Mucosa	stomach
29	chr18:12675800-12680000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr18:12676000-12682800	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr18:12676200-12686800	Strong transcription	Thymus	Thymus
32	chr18:12676400-12680400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr18:12676400-12682600	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr18:12676600-12680200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr18:12676600-12680200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr18:12676600-12680800	Strong transcription	Primary B cells from peripheral blood	blood
37	chr18:12676600-12681000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr18:12676600-12681000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr18:12676600-12682400	Strong transcription	Liver	Liver
40	chr18:12676600-12686800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr18:12676800-12680600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr18:12676800-12681200	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr18:12676800-12681400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr18:12677000-12680800	Strong transcription	Brain Germinal Matrix	brain
45	chr18:12677000-12686400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr18:12678200-12701400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr18:12678400-12685000	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr18:12678400-12685200	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr18:12678400-12686200	Weak transcription	Primary B cells from cord blood	blood
50	chr18:12678400-12686200	Weak transcription	K562	blood

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