Variant report

Variant	rs12969938
Chromosome Location	chr18:12705210-12705211
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:12701252..12704007-chr18:12704390..12707416,3	K562	blood:
2	chr18:12376201..12378120-chr18:12705040..12707340,2	K562	blood:
3	chr18:12700812..12705381-chr18:12946243..12950219,9	K562	blood:
4	chr18:12700615..12704798-chr18:12705051..12713643,12	MCF-7	breast:
5	chr18:12656018..12659900-chr18:12701056..12705601,5	K562	blood:

Variant related genes	Relation type
ENSG00000085415	Chromatin interaction
ENSG00000215527	Chromatin interaction
ENSG00000101624	Chromatin interaction
ENSG00000134278	Chromatin interaction
ENSG00000128789	Chromatin interaction
ENSG00000141385	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	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11080592	0.82[ASN][1000 genomes]
rs1129214	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12373207	0.90[ASN][1000 genomes]
rs12373259	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12455268	0.92[ASN][1000 genomes]
rs12455295	0.92[ASN][1000 genomes]
rs12457771	0.92[ASN][1000 genomes]
rs12458097	0.92[ASN][1000 genomes]
rs12458895	0.91[ASN][1000 genomes]
rs12954079	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12957555	0.92[ASN][1000 genomes]
rs12957603	0.92[ASN][1000 genomes]
rs12957810	0.92[ASN][1000 genomes]
rs12960623	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12960997	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12962598	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12963505	0.92[ASN][1000 genomes]
rs12964507	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12965733	0.94[ASN][1000 genomes]
rs12965990	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12966246	0.93[ASN][1000 genomes]
rs12966367	0.92[ASN][1000 genomes]
rs12966424	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12968771	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12969300	0.92[ASN][1000 genomes]
rs12969446	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12971256	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1362709	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1549011	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1592642	0.94[ASN][1000 genomes]
rs1592643	0.94[ASN][1000 genomes]
rs17616402	0.92[ASN][1000 genomes]
rs1971702	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2011575	0.92[ASN][1000 genomes]
rs2011579	0.92[ASN][1000 genomes]
rs2051262	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2302768	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28820339	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28832066	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34040888	0.89[ASN][1000 genomes]
rs34120824	0.92[ASN][1000 genomes]
rs34277169	0.92[ASN][1000 genomes]
rs34537593	0.89[ASN][1000 genomes]
rs34632667	0.91[ASN][1000 genomes]
rs34847769	0.91[ASN][1000 genomes]
rs35322088	0.91[ASN][1000 genomes]
rs35506854	0.92[ASN][1000 genomes]
rs35634465	0.85[ASN][1000 genomes]
rs35699948	0.92[ASN][1000 genomes]
rs35898717	0.89[ASN][1000 genomes]
rs3809919	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3902981	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4073592	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4296322	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs45589535	0.92[ASN][1000 genomes]
rs45596833	0.92[ASN][1000 genomes]
rs4633785	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55870255	0.92[ASN][1000 genomes]
rs62095975	0.92[ASN][1000 genomes]
rs62096023	0.92[ASN][1000 genomes]
rs62096046	0.89[ASN][1000 genomes]
rs62096048	0.86[ASN][1000 genomes]
rs6505760	0.94[ASN][1000 genomes]
rs66808227	0.92[ASN][1000 genomes]
rs7233175	0.91[ASN][1000 genomes]
rs7233694	0.92[ASN][1000 genomes]
rs7507018	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8083182	0.92[ASN][1000 genomes]
rs8083217	0.88[ASN][1000 genomes]
rs8086099	0.94[ASN][1000 genomes]
rs8086265	0.92[ASN][1000 genomes]
rs8097134	0.94[ASN][1000 genomes]
rs9303774	0.99[ASN][1000 genomes]
rs9303775	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9303776	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs933600	0.92[ASN][1000 genomes]
rs948319	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs963920	0.91[ASN][1000 genomes]
rs9945140	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9945644	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9945801	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9948844	0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs9949293	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9950365	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9951576	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9952000	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9954112	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9955985	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9957880	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9958100	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9958412	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9959039	0.92[ASN][1000 genomes]
rs9959458	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9959536	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9959611	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9960555	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9961799	0.94[ASN][1000 genomes]
rs9962006	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9963809	0.94[ASN][1000 genomes]
rs9964868	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9966464	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9966490	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9966672	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9967437	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9967553	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[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
rs12969938	CEP76	cis	Stomach	GTEx
rs12969938	SPIRE1	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12703400-12709000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr18:12703800-12713200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr18:12704000-12705400	Enhancers	Primary B cells from peripheral blood	blood
4	chr18:12704000-12705600	Enhancers	Spleen	Spleen
5	chr18:12704000-12706000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr18:12704000-12707400	Weak transcription	Lung	lung
7	chr18:12704200-12705600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr18:12704200-12705600	Enhancers	Primary T cells fromperipheralblood	blood
9	chr18:12704200-12705600	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr18:12704200-12705800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr18:12704200-12706200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr18:12704200-12706200	Weak transcription	Fetal Intestine Large	intestine
13	chr18:12704200-12706400	Weak transcription	Ovary	ovary
14	chr18:12704200-12707200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr18:12704200-12707200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr18:12704200-12707600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr18:12704200-12707600	Weak transcription	Esophagus	oesophagus
18	chr18:12704200-12709600	Weak transcription	HSMMtube	muscle
19	chr18:12704200-12709800	Weak transcription	Right Ventricle	heart
20	chr18:12704200-12713000	Weak transcription	Aorta	Aorta
21	chr18:12704200-12713200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr18:12704200-12713200	Weak transcription	Psoas Muscle	Psoas
23	chr18:12704200-12726800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr18:12704400-12705600	Enhancers	Brain Germinal Matrix	brain
25	chr18:12704400-12705800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr18:12704400-12705800	Enhancers	Fetal Brain Male	brain
27	chr18:12704400-12705800	Enhancers	Thymus	Thymus
28	chr18:12704400-12706000	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr18:12704400-12706000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr18:12704400-12706000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr18:12704400-12706200	Enhancers	HMEC	breast
32	chr18:12704400-12706400	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr18:12704400-12706800	Weak transcription	Fetal Kidney	kidney
34	chr18:12704400-12706800	Weak transcription	NHDF-Ad	bronchial
35	chr18:12704400-12707200	Weak transcription	Fetal Heart	heart
36	chr18:12704400-12707400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr18:12704400-12707400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr18:12704400-12707400	Weak transcription	Left Ventricle	heart
39	chr18:12704400-12707600	Weak transcription	Fetal Stomach	stomach
40	chr18:12704400-12710000	Weak transcription	NHLF	lung
41	chr18:12704600-12705600	Weak transcription	Primary hematopoietic stem cells	blood
42	chr18:12704600-12705800	Weak transcription	Placenta	Placenta
43	chr18:12704600-12706600	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr18:12704600-12706800	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr18:12704600-12707000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr18:12704600-12707000	Weak transcription	Fetal Muscle Trunk	muscle
47	chr18:12704600-12707600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr18:12704600-12708400	Weak transcription	Gastric	stomach
49	chr18:12704600-12713000	Weak transcription	Pancreas	Pancrea
50	chr18:12704800-12705400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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