Variant report

Variant	rs12888002
Chromosome Location	chr14:104238647-104238648
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1187417	0.85[EUR][1000 genomes]
rs12588797	0.85[EUR][1000 genomes]
rs12879529	0.81[EUR][1000 genomes]
rs12879612	0.81[ASN][1000 genomes]
rs12883337	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12885509	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12886637	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12890354	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12890430	0.82[EUR][1000 genomes]
rs12890822	0.83[EUR][1000 genomes]
rs12890837	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12893623	0.86[EUR][1000 genomes]
rs12894657	0.89[EUR][1000 genomes]
rs17791722	0.87[EUR][1000 genomes]
rs34596177	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35085624	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35740217	0.83[EUR][1000 genomes]
rs3742366	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3861678	0.82[EUR][1000 genomes]
rs4900597	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4906363	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4906364	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4906365	0.80[ASN][1000 genomes]
rs4906376	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4906377	0.88[EUR][1000 genomes]
rs4906378	0.82[EUR][1000 genomes]
rs4906379	0.85[EUR][1000 genomes]
rs56168984	0.86[EUR][1000 genomes]
rs6576006	0.82[EUR][1000 genomes]
rs6576007	0.83[EUR][1000 genomes]
rs66676135	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs66953418	0.89[EUR][1000 genomes]
rs7142769	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7143885	0.86[EUR][1000 genomes]
rs7149024	0.81[ASN][1000 genomes]
rs7156697	0.81[ASN][1000 genomes]
rs7156834	0.81[ASN][1000 genomes]
rs722637	0.90[EUR][1000 genomes]
rs8548	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9888591	0.93[EUR][1000 genomes];0.93[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	esv3332028	chr14:103581471-104328811	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
2	nsv1045162	chr14:104140525-104594841	Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv542204	chr14:104140525-104594841	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
4	esv2758368	chr14:104147525-104412813	Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	esv2760013	chr14:104147525-104412813	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
6	nsv902313	chr14:104162263-104378087	Bivalent Enhancer Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12888002	RP11-73M18.8	cis	Artery Tibial	GTEx

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:104196000-104268000	Weak transcription	Small Intestine	intestine
2	chr14:104201000-104267600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr14:104203200-104267800	Weak transcription	Psoas Muscle	Psoas
4	chr14:104208800-104260000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr14:104209400-104264800	Weak transcription	Brain Substantia Nigra	brain
6	chr14:104211800-104265000	Weak transcription	Hela-S3	cervix
7	chr14:104215000-104256800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr14:104215400-104248600	Weak transcription	Aorta	Aorta
9	chr14:104215400-104250000	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr14:104215400-104263800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr14:104215400-104273200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr14:104216000-104242600	Weak transcription	Colonic Mucosa	Colon
13	chr14:104216000-104267600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr14:104216200-104259000	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr14:104216200-104264400	Weak transcription	Brain Hippocampus Middle	brain
16	chr14:104216200-104264600	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr14:104216200-104267800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr14:104216200-104268800	Weak transcription	Brain Angular Gyrus	brain
19	chr14:104216400-104240600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr14:104216600-104254800	Weak transcription	Brain Anterior Caudate	brain
21	chr14:104216600-104257200	Weak transcription	HepG2	liver
22	chr14:104216800-104240800	Weak transcription	Fetal Intestine Large	intestine
23	chr14:104216800-104243600	Weak transcription	Pancreas	Pancrea
24	chr14:104216800-104261400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr14:104218400-104277800	Weak transcription	Spleen	Spleen
26	chr14:104218800-104243800	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr14:104218800-104270200	Weak transcription	Ovary	ovary
28	chr14:104219600-104250000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr14:104220200-104239200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr14:104220400-104241600	Weak transcription	Duodenum Mucosa	Duodenum
31	chr14:104220600-104246400	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr14:104223200-104254600	Weak transcription	HMEC	breast
33	chr14:104227600-104241400	Weak transcription	Placenta	Placenta
34	chr14:104228600-104243600	Weak transcription	Fetal Stomach	stomach
35	chr14:104228600-104265000	Weak transcription	Fetal Kidney	kidney
36	chr14:104228800-104245800	Weak transcription	A549	lung
37	chr14:104228800-104249800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr14:104228800-104263200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr14:104228800-104270200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr14:104229200-104267800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr14:104230600-104271600	Weak transcription	Esophagus	oesophagus
42	chr14:104230800-104239800	Weak transcription	Liver	Liver
43	chr14:104230800-104240000	Weak transcription	Fetal Heart	heart
44	chr14:104230800-104243600	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr14:104230800-104249200	Weak transcription	Stomach Smooth Muscle	stomach
46	chr14:104230800-104250400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr14:104232000-104245400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr14:104232000-104247200	Weak transcription	GM12878-XiMat	blood
49	chr14:104232000-104264000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr14:104232800-104250400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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