Variant report

Variant	rs12705090
Chromosome Location	chr7:100467700-100467701
allele	C/T
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	POLR2A	chr7:100467547-100468878	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr7:100467636-100468493	K562	blood:	n/a	n/a
3	POLR2A	chr7:100467670-100468710	K562	blood:	n/a	n/a
4	POLR2A	chr7:100467635-100467976	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
TRIP6	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12666989	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12667888	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12705089	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12705091	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12705092	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12705095	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12705096	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13226502	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13226864	0.93[EUR][1000 genomes]
rs13244629	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13245899	0.88[EUR][1000 genomes]
rs17881696	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17883557	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17884589	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs314324	0.84[ASN][1000 genomes]
rs314370	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs314373	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3757868	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6706	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829095	chr7:99814675-100494084	Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	393 gene(s)	inside rSNPs	diseases
2	nsv1020837	chr7:100313122-100508635	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	esv1832517	chr7:100355490-100749246	Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
4	esv2758125	chr7:100355490-100749246	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
5	esv2759547	chr7:100355490-100749246	Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
6	nsv464647	chr7:100374087-100497131	Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS 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	90 gene(s)	inside rSNPs	diseases
7	nsv607965	chr7:100374087-100497131	Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
8	nsv1032673	chr7:100382250-100606794	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
9	nsv888797	chr7:100386900-100482026	Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
10	nsv888798	chr7:100406144-100472826	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
11	nsv888799	chr7:100406144-100497131	Enhancers Bivalent Enhancer Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
12	nsv888801	chr7:100416250-100497131	Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
13	nsv464648	chr7:100422156-100518458	Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
14	nsv607966	chr7:100422156-100518458	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS 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	90 gene(s)	inside rSNPs	diseases
15	nsv831073	chr7:100425659-100544888	Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
16	esv3382561	chr7:100466516-100468564	Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12705090	ACHE	cis	Artery Tibial	GTEx
rs12705090	ACHE	cis	Nerve Tibial	GTEx
rs12705090	ACHE	cis	Artery Aorta	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100461800-100471400	Weak transcription	HepG2	liver
2	chr7:100465400-100467800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr7:100465600-100471800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr7:100465600-100471800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr7:100465600-100471800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr7:100465600-100472000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr7:100465800-100467800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr7:100465800-100469400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr7:100465800-100472000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr7:100466000-100467800	Weak transcription	Gastric	stomach
11	chr7:100466000-100468000	Weak transcription	Primary T cells from cord blood	blood
12	chr7:100466000-100468000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr7:100466000-100471600	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr7:100466000-100471800	Weak transcription	Fetal Brain Male	brain
15	chr7:100466200-100467800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr7:100466200-100467800	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr7:100466200-100468000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr7:100466200-100468000	Weak transcription	Duodenum Mucosa	Duodenum
19	chr7:100466200-100468200	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr7:100466200-100468400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr7:100466200-100468600	Weak transcription	Brain Anterior Caudate	brain
22	chr7:100466200-100468800	Weak transcription	Thymus	Thymus
23	chr7:100466200-100469000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr7:100466200-100471600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr7:100466200-100471600	Weak transcription	Brain Angular Gyrus	brain
26	chr7:100466200-100471600	Weak transcription	Brain Germinal Matrix	brain
27	chr7:100466200-100472000	Weak transcription	Fetal Kidney	kidney
28	chr7:100466400-100467800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr7:100466400-100467800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr7:100466400-100467800	Weak transcription	Aorta	Aorta
31	chr7:100466400-100467800	Weak transcription	Ovary	ovary
32	chr7:100466400-100467800	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr7:100466400-100468000	Weak transcription	Primary hematopoietic stem cells	blood
34	chr7:100466400-100468200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr7:100466400-100468200	Weak transcription	Left Ventricle	heart
36	chr7:100466400-100468200	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr7:100466400-100468400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr7:100466400-100468400	Weak transcription	A549	lung
39	chr7:100466400-100471600	Weak transcription	Primary B cells from peripheral blood	blood
40	chr7:100466400-100471600	Weak transcription	Right Atrium	heart
41	chr7:100466400-100471800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr7:100466400-100471800	Weak transcription	Fetal Heart	heart
43	chr7:100466600-100467800	Weak transcription	Brain Hippocampus Middle	brain
44	chr7:100466600-100467800	Weak transcription	Esophagus	oesophagus
45	chr7:100466600-100467800	Weak transcription	Right Ventricle	heart
46	chr7:100466600-100467800	Weak transcription	HSMMtube	muscle
47	chr7:100466600-100468000	Weak transcription	Placenta	Placenta
48	chr7:100466600-100468200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr7:100466600-100468200	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr7:100466600-100471000	Strong transcription	Spleen	Spleen

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