Variant report

Variant	rs12964507
Chromosome Location	chr18:12704056-12704057
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	WRNIP1	chr18:12703772-12704158	GM12878	blood:	n/a	n/a
2	TBP	chr18:12702207-12704065	GM12878	blood:	n/a	n/a
3	CHD1	chr18:12703869-12704147	GM12878	blood:	n/a	n/a
4	SIN3A	chr18:12702117-12704101	H1-hESC	embryonic stem cell:	n/a	chr18:12702466-12702475 chr18:12702672-12702681 chr18:12702665-12702678
5	MXI1	chr18:12702009-12704247	SK-N-SH	brain:	n/a	n/a
6	HCFC1	chr18:12702200-12704089	Hela-S3	cervix:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr18:12375309..12380137-chr18:12701387..12704274,11	K562	blood:
2	chr18:12701407..12705081-chr18:12945993..12949483,5	MCF-7	breast:
3	chr18:12696763..12699239-chr18:12701108..12704411,4	MCF-7	breast:
4	chr18:12700812..12705381-chr18:12946243..12950219,9	K562	blood:
5	chr18:12689483..12696263-chr18:12698961..12704404,9	MCF-7	breast:
6	chr18:12375314..12379217-chr18:12700733..12704866,11	K562	blood:
7	chr18:12700182..12704223-chr18:12944670..12949511,9	K562	blood:
8	chr18:12702487..12704134-chr18:12881395..12884232,2	MCF-7	breast:
9	chr18:12376063..12377849-chr18:12702588..12704602,2	MCF-7	breast:
10	chr12:120729381..120730900-chr18:12702467..12704438,2	MCF-7	breast:
11	chr18:12656018..12659900-chr18:12701056..12705601,5	K562	blood:
12	chr18:12702796..12704703-chr18:12947568..12949253,2	MCF-7	breast:

No data

Variant related genes	Relation type
CEP76	TF binding region
ENSG00000141385	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000215527	Chromatin interaction
ENSG00000128789	Chromatin interaction
ENSG00000101624	Chromatin interaction
ENSG00000134278	Chromatin interaction
ENSG00000085415	Chromatin interaction
ENSG00000175354	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs1062235	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11080592	0.82[ASN][1000 genomes]
rs1129214	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12373207	0.89[ASN][1000 genomes]
rs12373259	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12455268	0.91[ASN][1000 genomes]
rs12455295	0.91[ASN][1000 genomes]
rs12457771	0.91[ASN][1000 genomes]
rs12458097	0.91[ASN][1000 genomes]
rs12458895	0.91[ASN][1000 genomes]
rs12954079	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12957555	0.91[ASN][1000 genomes]
rs12957603	0.91[ASN][1000 genomes]
rs12957810	0.91[ASN][1000 genomes]
rs12960623	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12960997	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12962598	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12963505	0.91[ASN][1000 genomes]
rs12965733	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12965990	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12966246	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs12966367	0.91[ASN][1000 genomes]
rs12966424	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12968771	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12969300	0.91[ASN][1000 genomes]
rs12969446	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12969938	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12971256	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1362709	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1549011	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1592642	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1592643	0.93[ASN][1000 genomes]
rs17616402	0.91[ASN][1000 genomes]
rs1971702	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2011575	0.91[ASN][1000 genomes]
rs2011579	0.91[ASN][1000 genomes]
rs2051262	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2302768	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28820339	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28832066	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34040888	0.88[ASN][1000 genomes]
rs34120824	0.91[ASN][1000 genomes]
rs34277169	0.91[ASN][1000 genomes]
rs34537593	0.88[ASN][1000 genomes]
rs34632667	0.90[ASN][1000 genomes]
rs34847769	0.91[ASN][1000 genomes]
rs35322088	0.90[ASN][1000 genomes]
rs35506854	0.91[ASN][1000 genomes]
rs35634465	0.84[ASN][1000 genomes]
rs35699948	0.91[ASN][1000 genomes]
rs35898717	0.88[ASN][1000 genomes]
rs3809919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3902981	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4073592	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4296322	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs45589535	0.91[ASN][1000 genomes]
rs45596833	0.91[ASN][1000 genomes]
rs4633785	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55870255	0.91[ASN][1000 genomes]
rs62095975	0.91[ASN][1000 genomes]
rs62096023	0.91[ASN][1000 genomes]
rs62096046	0.88[ASN][1000 genomes]
rs62096048	0.85[ASN][1000 genomes]
rs6505760	0.93[ASN][1000 genomes]
rs66808227	0.91[ASN][1000 genomes]
rs7233175	0.90[ASN][1000 genomes]
rs7233694	0.91[ASN][1000 genomes]
rs7507018	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8083182	0.91[ASN][1000 genomes]
rs8083217	0.87[ASN][1000 genomes]
rs8086099	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs8086265	0.91[ASN][1000 genomes]
rs8097134	0.93[ASN][1000 genomes]
rs9303774	0.98[ASN][1000 genomes]
rs9303775	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9303776	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs933600	0.91[ASN][1000 genomes]
rs948319	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs963920	0.91[ASN][1000 genomes]
rs9945140	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9945644	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9945801	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9948844	0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs9949293	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9950365	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9951576	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9952000	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9954112	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9955985	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9957880	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9958100	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9958412	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9959039	0.91[ASN][1000 genomes]
rs9959458	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9959536	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9959611	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9960555	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9961799	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs9962006	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9963809	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs9964868	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9966464	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9966490	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9966672	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9967437	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9967553	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
10	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
11	nsv1064273	chr18:12697601-12828251	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12964507	SPIRE1	cis	Muscle Skeletal	GTEx
rs12964507	CEP76	cis	Stomach	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12701200-12704400	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr18:12701600-12704200	Active TSS	Aorta	Aorta
3	chr18:12701600-12704200	Active TSS	Esophagus	oesophagus
4	chr18:12701800-12704200	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr18:12701800-12704200	Active TSS	Ovary	ovary
6	chr18:12701800-12704400	Active TSS	GM12878-XiMat	blood
7	chr18:12701800-12704800	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr18:12702000-12704400	Active TSS	Left Ventricle	heart
9	chr18:12702200-12704200	Active TSS	Fetal Muscle Trunk	muscle
10	chr18:12703000-12704400	Active TSS	Right Atrium	heart
11	chr18:12703200-12704800	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr18:12703400-12704200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
13	chr18:12703400-12704400	Flanking Active TSS	Adipose Nuclei	Adipose
14	chr18:12703400-12704800	Flanking Active TSS	Primary T cells from cord blood	blood
15	chr18:12703400-12704800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr18:12703400-12709000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr18:12703600-12704200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
18	chr18:12703600-12704200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr18:12703600-12704200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
20	chr18:12703600-12704200	Flanking Active TSS	Liver	Liver
21	chr18:12703600-12704200	Flanking Active TSS	Brain Angular Gyrus	brain
22	chr18:12703600-12704200	Flanking Active TSS	Brain Anterior Caudate	brain
23	chr18:12703600-12704200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
24	chr18:12703600-12704200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr18:12703600-12704200	Flanking Active TSS	Colon Smooth Muscle	Colon
26	chr18:12703600-12704200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
27	chr18:12703600-12704200	Flanking Active TSS	Fetal Stomach	stomach
28	chr18:12703600-12704200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
29	chr18:12703600-12704200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
30	chr18:12703600-12704400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
31	chr18:12703600-12704400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
32	chr18:12703600-12704400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr18:12703600-12704400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr18:12703600-12704400	Flanking Active TSS	Brain Hippocampus Middle	brain
35	chr18:12703600-12704400	Flanking Active TSS	Duodenum Mucosa	Duodenum
36	chr18:12703600-12704400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr18:12703600-12704400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr18:12703600-12704600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr18:12703600-12704600	Flanking Active TSS	Primary hematopoietic stem cells	blood
40	chr18:12703600-12704600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
41	chr18:12703600-12704600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr18:12703600-12704600	Flanking Active TSS	Fetal Brain Female	brain
43	chr18:12703600-12704800	Flanking Active TSS	Dnd41	blood
44	chr18:12703800-12704200	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr18:12703800-12704200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr18:12703800-12704200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
47	chr18:12703800-12704200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
48	chr18:12703800-12704200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
49	chr18:12703800-12704200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
50	chr18:12703800-12704200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood

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