Variant report

Variant	rs2682426
Chromosome Location	chr12:123653556-123653557
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:123652587..123654212-chr12:123716240..123718680,2	K562	blood:

Variant related genes	Relation type
ENSG00000051825	Chromatin interaction
ENSG00000130921	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1047158	0.83[AMR][1000 genomes]
rs1051431	0.83[AMR][1000 genomes]
rs10772995	0.84[AMR][1000 genomes]
rs10772998	0.80[AMR][1000 genomes]
rs10846478	0.85[AMR][1000 genomes]
rs11057192	0.84[AMR][1000 genomes]
rs11057206	0.80[AMR][1000 genomes]
rs11057210	0.80[AMR][1000 genomes]
rs1402274	0.85[AMR][1000 genomes]
rs1615694	0.85[AMR][1000 genomes]
rs1621194	0.83[AMR][1000 genomes]
rs1626899	0.82[AMR][1000 genomes]
rs1630693	0.80[AMR][1000 genomes]
rs1630905	0.82[AMR][1000 genomes]
rs1716156	0.84[AMR][1000 genomes]
rs1716157	0.85[AMR][1000 genomes]
rs1716159	0.84[AMR][1000 genomes]
rs1716160	0.82[AMR][1000 genomes]
rs1716164	0.84[AMR][1000 genomes]
rs1716165	0.83[AMR][1000 genomes]
rs1716167	0.83[AMR][1000 genomes]
rs1716168	0.83[AMR][1000 genomes]
rs1716170	0.82[AMR][1000 genomes]
rs1716171	0.82[AMR][1000 genomes]
rs1716172	0.82[AMR][1000 genomes]
rs1716173	0.84[AMR][1000 genomes]
rs1716175	0.87[AMR][1000 genomes]
rs1716176	0.88[AMR][1000 genomes]
rs1716177	0.88[AMR][1000 genomes]
rs1716182	0.85[AMR][1000 genomes]
rs1716185	0.81[AMR][1000 genomes]
rs1727290	0.85[AMR][1000 genomes]
rs1727296	0.83[AMR][1000 genomes]
rs1727300	0.84[AMR][1000 genomes]
rs1727306	0.84[AMR][1000 genomes]
rs1727314	0.83[AMR][1000 genomes]
rs1727315	0.81[AMR][1000 genomes]
rs1727320	0.82[AMR][1000 genomes]
rs1727323	0.84[AMR][1000 genomes]
rs1727325	0.83[AMR][1000 genomes]
rs1727334	0.82[AMR][1000 genomes]
rs1790086	0.85[AMR][1000 genomes]
rs1790087	0.85[AMR][1000 genomes]
rs1790089	0.85[AMR][1000 genomes]
rs1790095	0.85[AMR][1000 genomes]
rs1790098	0.88[AMR][1000 genomes]
rs1790100	0.88[AMR][1000 genomes]
rs1790101	0.82[AMR][1000 genomes]
rs1790102	0.83[AMR][1000 genomes]
rs1790108	0.81[AMR][1000 genomes]
rs1790109	0.81[AMR][1000 genomes]
rs1790124	0.84[AMR][1000 genomes]
rs1790130	0.82[AMR][1000 genomes]
rs1790131	0.82[AMR][1000 genomes]
rs2049114	0.87[AMR][1000 genomes]
rs2682429	0.83[AMR][1000 genomes]
rs2682430	0.82[AMR][1000 genomes]
rs2682431	0.82[AMR][1000 genomes]
rs2682434	0.84[AMR][1000 genomes]
rs2695481	0.83[AMR][1000 genomes]
rs2851436	0.84[AMR][1000 genomes]
rs2851438	0.83[AMR][1000 genomes]
rs2950537	0.88[AMR][1000 genomes]
rs3018098	0.88[AMR][1000 genomes]
rs4372492	0.84[AMR][1000 genomes]
rs4759409	0.80[AMR][1000 genomes]
rs941305	0.82[AMR][1000 genomes]
rs941306	0.82[AMR][1000 genomes]
rs9795522	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS 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 miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	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
4	nsv1042550	chr12:123532028-123659500	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2682426	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs2682426	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs2682426	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs2682426	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs2682426	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs2682426	LOC283378	Cis_1M	lymphoblastoid	RTeQTL
rs2682426	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 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	chr12:123640600-123657800	Weak transcription	NHLF	lung
14	chr12:123645400-123660000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:123645600-123660800	Weak transcription	Fetal Brain Male	brain
16	chr12:123647400-123655000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr12:123647400-123660800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr12:123648400-123656200	Strong transcription	Fetal Stomach	stomach
19	chr12:123648400-123679200	Strong transcription	Thymus	Thymus
20	chr12:123648800-123673600	Weak transcription	HMEC	breast
21	chr12:123649000-123658400	Weak transcription	HUVEC	blood vessel
22	chr12:123649200-123660800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr12:123650000-123660600	Weak transcription	Fetal Kidney	kidney
24	chr12:123650400-123686400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr12:123650600-123655000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr12:123650600-123655000	Weak transcription	Fetal Lung	lung
27	chr12:123650600-123655000	Weak transcription	A549	lung
28	chr12:123650600-123655200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr12:123650600-123658000	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr12:123650600-123658000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr12:123650600-123660800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr12:123650600-123660800	Weak transcription	HSMM	muscle
33	chr12:123650600-123664600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr12:123650600-123664600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr12:123650600-123671600	Weak transcription	Brain Germinal Matrix	brain
36	chr12:123650600-123673600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr12:123650600-123685800	Weak transcription	Small Intestine	intestine
38	chr12:123650600-123687200	Weak transcription	Pancreas	Pancrea
39	chr12:123650600-123716400	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr12:123650800-123654600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr12:123650800-123655000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr12:123650800-123657800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr12:123650800-123657800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr12:123650800-123663600	Weak transcription	Lung	lung
45	chr12:123651000-123658000	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr12:123651200-123654400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr12:123651200-123655200	Weak transcription	NH-A	brain
48	chr12:123651200-123659400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr12:123651200-123660800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr12:123651200-123661200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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