Variant report

Variant	rs34040888
Chromosome Location	chr18:12727143-12727144
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Distal block	Cell Line	Cell type
1	chr18:12725367..12727823-chr18:12887215..12889210,2	K562	blood:
2	chr18:12726771..12727633-chr18:12766775..12767717,3	MCF-7	breast:
3	chr18:12726736..12727393-chr18:12846308..12846890,2	MCF-7	breast:
4	chr18:12726304..12729223-chr18:12948825..12951791,2	K562	blood:
5	chr18:12689725..12692648-chr18:12725870..12727791,2	K562	blood:
6	chr18:12726857..12727908-chr18:12766755..12767707,3	K562	blood:
7	chr18:12726793..12727997-chr18:12893494..12894384,4	K562	blood:
8	chr18:12726635..12727970-chr18:12934143..12935576,12	K562	blood:
9	chr18:12725757..12728002-chr18:12765870..12768020,2	K562	blood:
10	chr18:12726953..12727699-chr18:12934094..12935046,3	MCF-7	breast:
11	chr18:12391605..12392308-chr18:12726671..12727207,2	K562	blood:
12	chr18:12720684..12722477-chr18:12725807..12728558,2	MCF-7	breast:

No data

Extended variants
information (count: 116 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1062235	0.89[ASN][1000 genomes]
rs1129214	0.89[ASN][1000 genomes]
rs12373207	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12373259	0.87[ASN][1000 genomes]
rs12454322	0.80[EUR][1000 genomes]
rs12455268	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12455295	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12457771	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12458097	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12458895	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12954079	0.89[ASN][1000 genomes]
rs12957555	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12957603	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12957810	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12960623	0.96[ASN][1000 genomes]
rs12960997	0.89[ASN][1000 genomes]
rs12962598	0.89[ASN][1000 genomes]
rs12963505	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12964507	0.88[ASN][1000 genomes]
rs12965733	0.84[ASN][1000 genomes]
rs12965990	0.89[ASN][1000 genomes]
rs12966246	0.83[ASN][1000 genomes]
rs12966367	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12966424	0.89[ASN][1000 genomes]
rs12968771	0.96[ASN][1000 genomes]
rs12969300	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12969446	0.89[ASN][1000 genomes]
rs12969938	0.89[ASN][1000 genomes]
rs12971256	0.84[ASN][1000 genomes]
rs1362709	0.90[ASN][1000 genomes]
rs1549011	0.89[ASN][1000 genomes]
rs1592642	0.84[ASN][1000 genomes]
rs1592643	0.84[ASN][1000 genomes]
rs17616402	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1971702	0.83[ASN][1000 genomes]
rs2011575	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2011579	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2051262	0.88[ASN][1000 genomes]
rs2302768	0.90[ASN][1000 genomes]
rs28820339	0.84[ASN][1000 genomes]
rs28832066	0.89[ASN][1000 genomes]
rs34120824	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34277169	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34472716	0.81[ASN][1000 genomes]
rs34537593	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34632667	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34690304	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34847769	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35322088	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35506854	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35634465	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35699948	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35898717	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3809919	0.88[ASN][1000 genomes]
rs3902981	0.81[ASN][1000 genomes]
rs4296322	0.88[ASN][1000 genomes]
rs45589535	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs45596833	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4633785	0.89[ASN][1000 genomes]
rs55870255	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62095975	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62096023	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62096046	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62096048	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6505760	0.84[ASN][1000 genomes]
rs66808227	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7233175	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7233694	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7507018	0.89[ASN][1000 genomes]
rs8083182	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8086099	0.84[ASN][1000 genomes]
rs8086265	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8086846	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8097134	0.84[ASN][1000 genomes]
rs9303774	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9303775	0.89[ASN][1000 genomes]
rs9303776	0.87[ASN][1000 genomes]
rs933600	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs948319	0.90[ASN][1000 genomes]
rs963920	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9945140	0.89[ASN][1000 genomes]
rs9945644	0.89[ASN][1000 genomes]
rs9945801	0.89[ASN][1000 genomes]
rs9948844	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9949293	0.89[ASN][1000 genomes]
rs9950365	0.89[ASN][1000 genomes]
rs9951576	0.89[ASN][1000 genomes]
rs9952000	0.89[ASN][1000 genomes]
rs9954112	0.89[ASN][1000 genomes]
rs9955985	0.89[ASN][1000 genomes]
rs9957880	0.88[ASN][1000 genomes]
rs9958100	0.90[ASN][1000 genomes]
rs9958412	0.89[ASN][1000 genomes]
rs9959039	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9959458	0.89[ASN][1000 genomes]
rs9959536	0.88[ASN][1000 genomes]
rs9960555	0.88[ASN][1000 genomes]
rs9961799	0.84[ASN][1000 genomes]
rs9962006	0.89[ASN][1000 genomes]
rs9963809	0.84[ASN][1000 genomes]
rs9964868	0.92[ASN][1000 genomes]
rs9966464	0.88[ASN][1000 genomes]
rs9966490	0.90[ASN][1000 genomes]
rs9966672	0.90[ASN][1000 genomes]
rs9967437	0.89[ASN][1000 genomes]
rs9967553	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
7	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
8	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
9	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
10	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs34040888	RP11-861E21.2	cis	Muscle Skeletal	GTEx
rs34040888	SPIRE1	cis	Muscle Skeletal	GTEx
rs34040888	TNFSF5IP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12704800-12727200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr18:12704800-12727800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr18:12705000-12728600	Weak transcription	Stomach Mucosa	stomach
4	chr18:12705400-12727200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr18:12705600-12727200	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr18:12705600-12727200	Strong transcription	Duodenum Mucosa	Duodenum
7	chr18:12705600-12727200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr18:12705800-12727200	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr18:12705800-12727200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr18:12705800-12727200	Strong transcription	Fetal Muscle Leg	muscle
11	chr18:12706000-12727200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr18:12706200-12727200	Strong transcription	Primary T helper cells PMA-I stimulated	--
13	chr18:12706200-12727200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr18:12706400-12727200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr18:12706600-12727200	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr18:12706600-12727200	Strong transcription	Adipose Nuclei	Adipose
17	chr18:12710200-12727200	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr18:12710200-12727200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr18:12712800-12727200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr18:12714600-12728800	Weak transcription	Esophagus	oesophagus
21	chr18:12717000-12727200	Strong transcription	Primary B cells from peripheral blood	blood
22	chr18:12717200-12727200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr18:12717400-12727200	Strong transcription	Left Ventricle	heart
24	chr18:12717600-12727200	Strong transcription	Fetal Lung	lung
25	chr18:12718400-12727200	Strong transcription	Fetal Muscle Trunk	muscle
26	chr18:12718600-12727200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr18:12719000-12727800	Strong transcription	Sigmoid Colon	Sigmoid Colon
28	chr18:12720000-12727200	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr18:12720000-12727200	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr18:12720600-12727800	Strong transcription	HUVEC	blood vessel
31	chr18:12721800-12727200	Strong transcription	Primary B cells from cord blood	blood
32	chr18:12721800-12728200	Strong transcription	HSMM	muscle
33	chr18:12722200-12727200	Strong transcription	Placenta Amnion	Placenta Amnion
34	chr18:12723000-12728600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr18:12723000-12748400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr18:12723200-12728600	Weak transcription	Aorta	Aorta
37	chr18:12723400-12728200	Weak transcription	Small Intestine	intestine
38	chr18:12723400-12728600	Weak transcription	Colon Smooth Muscle	Colon
39	chr18:12723600-12728400	Weak transcription	Rectal Smooth Muscle	rectum
40	chr18:12724200-12730000	Weak transcription	K562	blood
41	chr18:12724600-12728200	Weak transcription	Fetal Kidney	kidney
42	chr18:12724600-12728400	Weak transcription	Psoas Muscle	Psoas
43	chr18:12724600-12728600	Weak transcription	Ovary	ovary
44	chr18:12724600-12729600	Weak transcription	Fetal Brain Female	brain
45	chr18:12724600-12729800	Weak transcription	HSMMtube	muscle
46	chr18:12724800-12728000	Weak transcription	NHLF	lung
47	chr18:12725000-12727800	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr18:12725000-12728600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr18:12725200-12729600	Weak transcription	Brain Cingulate Gyrus	brain
50	chr18:12725200-12730200	Weak transcription	A549	lung

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