Variant report

Variant	rs1716174
Chromosome Location	chr12:123660717-123660718
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10772995	0.81[EUR][1000 genomes]
rs10846478	0.81[EUR][1000 genomes]
rs1615694	0.80[EUR][1000 genomes]
rs1716157	0.81[EUR][1000 genomes]
rs1716158	0.86[EUR][1000 genomes]
rs1716159	0.81[EUR][1000 genomes]
rs1716173	0.84[EUR][1000 genomes]
rs1716175	0.81[EUR][1000 genomes]
rs1716182	0.81[EUR][1000 genomes]
rs1727306	0.81[EUR][1000 genomes]
rs1727309	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1727310	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1727311	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1727322	0.82[EUR][1000 genomes]
rs1790086	0.81[EUR][1000 genomes]
rs1790087	0.81[EUR][1000 genomes]
rs1790123	0.83[EUR][1000 genomes]
rs2049114	0.81[EUR][1000 genomes]
rs2682433	0.88[AFR][1000 genomes]
rs2695476	0.88[AFR][1000 genomes]
rs2695478	0.81[EUR][1000 genomes]
rs2695479	0.88[AFR][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	nsv427924	chr12:123412172-123722059	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
2	esv1825473	chr12:123582855-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv870326	chr12:123585990-123719323	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv2761773	chr12:123616003-123723460	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	esv1803368	chr12:123640853-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
6	esv1830566	chr12:123640853-123822503	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers 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	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1716174	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs1716174	CDK2AP1	cis	Skin Sun Exposed Lower leg	GTEx
rs1716174	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs1716174	CDK2AP1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123636600-123660800	Weak transcription	Colon Smooth Muscle	Colon
2	chr12:123636600-123676200	Weak transcription	Gastric	stomach
3	chr12:123636600-123716600	Weak transcription	Esophagus	oesophagus
4	chr12:123636800-123675200	Weak transcription	Fetal Heart	heart
5	chr12:123636800-123679600	Weak transcription	Colonic Mucosa	Colon
6	chr12:123636800-123687400	Weak transcription	Psoas Muscle	Psoas
7	chr12:123637000-123673400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr12:123637000-123713000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr12:123637200-123716400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr12:123638600-123687200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:123638800-123685000	Strong transcription	Fetal Thymus	thymus
12	chr12:123640400-123676000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr12:123645600-123660800	Weak transcription	Fetal Brain Male	brain
14	chr12:123647400-123660800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr12:123648400-123679200	Strong transcription	Thymus	Thymus
16	chr12:123648800-123673600	Weak transcription	HMEC	breast
17	chr12:123649200-123660800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr12:123650400-123686400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr12:123650600-123660800	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr12:123650600-123660800	Weak transcription	HSMM	muscle
21	chr12:123650600-123664600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr12:123650600-123664600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr12:123650600-123671600	Weak transcription	Brain Germinal Matrix	brain
24	chr12:123650600-123673600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr12:123650600-123685800	Weak transcription	Small Intestine	intestine
26	chr12:123650600-123687200	Weak transcription	Pancreas	Pancrea
27	chr12:123650600-123716400	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr12:123650800-123663600	Weak transcription	Lung	lung
29	chr12:123651200-123660800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr12:123651200-123661200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr12:123651200-123670000	Weak transcription	Spleen	Spleen
32	chr12:123651200-123673600	Weak transcription	Brain Substantia Nigra	brain
33	chr12:123651400-123660800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr12:123651400-123660800	Weak transcription	Osteobl	bone
35	chr12:123651400-123662600	Weak transcription	Brain Anterior Caudate	brain
36	chr12:123651400-123663200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr12:123651400-123672000	Weak transcription	NHDF-Ad	bronchial
38	chr12:123651400-123673600	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr12:123651400-123673600	Weak transcription	NHEK	skin
40	chr12:123651400-123675800	Weak transcription	Ovary	ovary
41	chr12:123651600-123663600	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr12:123651600-123676000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr12:123652000-123673000	Weak transcription	Aorta	Aorta
44	chr12:123652200-123676200	Weak transcription	Right Ventricle	heart
45	chr12:123652400-123661000	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr12:123652400-123661600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr12:123652400-123665600	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr12:123652600-123672800	Weak transcription	Brain Cingulate Gyrus	brain
49	chr12:123652800-123662600	Weak transcription	Brain Angular Gyrus	brain
50	chr12:123652800-123707800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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