Variant report

Variant	rs2296563
Chromosome Location	chr14:67859681-67859682
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	CEBPB	chr14:67859497-67859793	HepG2	liver:	n/a	n/a
2	POLR2A	chr14:67859021-67859745	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
PLEK2	TF binding region

Extended variants
information (count: 118 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10129185	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10131175	0.89[AMR][1000 genomes]
rs10132093	0.91[ASN][1000 genomes]
rs10135163	0.86[AMR][1000 genomes]
rs10135498	0.89[AMR][1000 genomes]
rs10136710	0.86[AMR][1000 genomes]
rs10137557	0.89[AMR][1000 genomes]
rs10138755	0.89[AMR][1000 genomes]
rs10139585	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10139684	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10139953	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10141180	0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10143251	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10144122	0.93[ASN][1000 genomes]
rs10144417	0.89[AMR][1000 genomes]
rs10144774	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10146389	0.86[ASN][1000 genomes]
rs10149615	0.90[ASN][1000 genomes]
rs1044745	0.86[ASN][1000 genomes]
rs1044750	0.83[AMR][1000 genomes]
rs1045060	0.86[AMR][1000 genomes]
rs12587679	0.83[AMR][1000 genomes]
rs12588292	0.93[ASN][1000 genomes]
rs12588458	0.91[ASN][1000 genomes]
rs12588478	0.84[AMR][1000 genomes]
rs12589671	0.89[AMR][1000 genomes]
rs12589983	0.84[AMR][1000 genomes]
rs12590065	0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12590952	0.86[AMR][1000 genomes]
rs13379142	0.89[AMR][1000 genomes]
rs13379368	0.89[AMR][1000 genomes]
rs1473732	0.83[ASN][1000 genomes]
rs1536271	0.89[AMR][1000 genomes]
rs1536272	0.89[AMR][1000 genomes]
rs1536273	0.89[AMR][1000 genomes]
rs17104202	0.83[ASN][1000 genomes]
rs17248714	0.89[AMR][1000 genomes]
rs1885590	0.87[ASN][1000 genomes]
rs1980817	0.86[AMR][1000 genomes]
rs2031563	0.89[AMR][1000 genomes]
rs2031564	0.90[ASN][1000 genomes]
rs2094162	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2148160	0.81[ASN][1000 genomes]
rs2236333	0.86[AMR][1000 genomes]
rs2274335	0.86[AMR][1000 genomes]
rs2274336	0.89[AMR][1000 genomes]
rs2274338	0.89[AMR][1000 genomes]
rs2296560	0.89[AMR][1000 genomes]
rs2296561	0.91[ASN][1000 genomes]
rs2296562	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2319777	0.89[ASN][1000 genomes]
rs28422832	0.89[AMR][1000 genomes]
rs28441403	0.83[AMR][1000 genomes]
rs28456209	0.89[AMR][1000 genomes]
rs28458235	0.86[AMR][1000 genomes]
rs28558916	0.89[AMR][1000 genomes]
rs28668536	0.89[AMR][1000 genomes]
rs28866617	0.81[AMR][1000 genomes]
rs3759755	0.89[AMR][1000 genomes]
rs3784085	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3818467	0.89[AMR][1000 genomes]
rs3818468	0.86[AMR][1000 genomes]
rs3825722	0.89[AMR][1000 genomes]
rs57154550	0.88[ASN][1000 genomes]
rs57234033	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs58257525	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs60505324	0.85[ASN][1000 genomes]
rs6573765	0.83[ASN][1000 genomes]
rs6573768	0.90[ASN][1000 genomes]
rs6573769	0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6573770	0.80[ASN][1000 genomes]
rs66851210	0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs67968914	0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs68002629	0.92[ASN][1000 genomes]
rs7153350	0.83[AMR][1000 genomes]
rs7153725	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7154607	0.96[ASN][1000 genomes]
rs7156441	0.89[AMR][1000 genomes]
rs7157704	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72476727	0.81[AMR][1000 genomes]
rs73280987	0.84[ASN][1000 genomes]
rs73282707	0.90[ASN][1000 genomes]
rs73284810	0.84[AMR][1000 genomes]
rs73284812	0.86[AMR][1000 genomes]
rs73284892	0.87[ASN][1000 genomes]
rs8003327	0.93[ASN][1000 genomes]
rs8004332	0.83[AMR][1000 genomes]
rs8004864	0.83[AMR][1000 genomes]
rs8005756	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8005876	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8005900	0.83[AMR][1000 genomes]
rs8006042	0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs8006391	0.89[AMR][1000 genomes]
rs8006519	0.89[AMR][1000 genomes]
rs8007033	0.89[AMR][1000 genomes]
rs8007696	0.90[ASN][1000 genomes]
rs8007866	0.93[ASN][1000 genomes]
rs8008443	0.82[ASN][1000 genomes]
rs8008619	0.89[AMR][1000 genomes]
rs8008724	0.89[AMR][1000 genomes]
rs8015641	0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs8015819	0.87[ASN][1000 genomes]
rs8016024	0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs8016623	0.86[AMR][1000 genomes]
rs8019109	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs8020720	0.86[AMR][1000 genomes]
rs8020850	0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs8021621	0.83[AMR][1000 genomes]
rs8021992	0.81[ASN][1000 genomes]
rs960797	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9743912	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751285	chr14:67364747-67886781	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv1045518	chr14:67529049-67959582	Strong transcription Bivalent Enhancer Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv456331	chr14:67732861-68103780	Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv564961	chr14:67732861-68103780	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv470651	chr14:67732861-68113293	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
6	nsv1054389	chr14:67804987-67922598	Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
7	nsv542121	chr14:67804987-67922598	Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2296563	EIF2S1	Cis_1M	lymphoblastoid	RTeQTL
rs2296563	ATP6V1D	cis	Thyroid	GTEx
rs2296563	ATP6V1D	cis	lung	GTEx

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:67831200-67864600	Strong transcription	Duodenum Mucosa	Duodenum
2	chr14:67835200-67863400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr14:67837600-67860800	Strong transcription	Sigmoid Colon	Sigmoid Colon
4	chr14:67839600-67862400	Strong transcription	Fetal Intestine Large	intestine
5	chr14:67845000-67864800	Strong transcription	Hela-S3	cervix
6	chr14:67846000-67876200	Weak transcription	Stomach Mucosa	stomach
7	chr14:67849200-67860600	Strong transcription	Fetal Stomach	stomach
8	chr14:67849600-67864400	Weak transcription	Gastric	stomach
9	chr14:67850000-67862200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr14:67850200-67878400	Weak transcription	Lung	lung
11	chr14:67850600-67862400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr14:67851000-67863200	Weak transcription	Fetal Lung	lung
13	chr14:67852000-67860200	Weak transcription	NHLF	lung
14	chr14:67852200-67862400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr14:67852200-67863200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr14:67852400-67862400	Weak transcription	HSMMtube	muscle
17	chr14:67852600-67862000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr14:67852800-67863200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr14:67852800-67865800	Strong transcription	HMEC	breast
20	chr14:67853200-67862600	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr14:67853800-67862800	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr14:67853800-67864600	Strong transcription	Fetal Intestine Small	intestine
23	chr14:67854000-67861600	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr14:67854000-67862400	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr14:67854000-67863000	Weak transcription	HSMM	muscle
26	chr14:67854200-67861800	Weak transcription	HUVEC	blood vessel
27	chr14:67854200-67862600	Weak transcription	NH-A	brain
28	chr14:67854200-67864400	Weak transcription	Left Ventricle	heart
29	chr14:67854200-67872000	Weak transcription	Small Intestine	intestine
30	chr14:67854400-67863200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr14:67854600-67862600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr14:67855200-67861800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr14:67855200-67863200	Weak transcription	A549	lung
34	chr14:67855200-67867400	Strong transcription	NHEK	skin
35	chr14:67855200-67875400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr14:67856000-67861200	Enhancers	Fetal Thymus	thymus
37	chr14:67857000-67862000	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr14:67857000-67862200	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr14:67857200-67860000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr14:67857200-67860000	Enhancers	Placenta	Placenta
41	chr14:67858000-67859800	Enhancers	K562	blood
42	chr14:67858400-67860000	Enhancers	HepG2	liver
43	chr14:67858400-67860200	Strong transcription	Colonic Mucosa	Colon
44	chr14:67858600-67867400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr14:67858800-67859800	Enhancers	Spleen	Spleen
46	chr14:67858800-67861200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr14:67859200-67859800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr14:67859200-67860000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr14:67859200-67860200	Enhancers	Liver	Liver
50	chr14:67859200-67861200	Weak transcription	Fetal Heart	heart

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