Variant report

Variant	rs2337630
Chromosome Location	chr12:123733086-123733087
allele	A/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	NFYB	chr12:123733049-123733684	K562	blood:	n/a	n/a
2	SETDB1	chr12:123732563-123733210	U2OS	brain:	n/a	n/a
3	CBX3	chr12:123732611-123733220	K562	blood:	n/a	n/a

Variant related genes	Relation type
MPHOSPH9	TF binding region
C12orf65	TF binding region

Extended variants
information (count: 55 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1051434	0.82[AFR][1000 genomes]
rs10772999	0.83[ASN][1000 genomes]
rs10773000	0.94[ASN][1000 genomes]
rs10846489	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11057205	0.83[ASN][1000 genomes]
rs11057207	0.83[ASN][1000 genomes]
rs11057209	0.84[ASN][1000 genomes]
rs11057219	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11057223	0.84[ASN][1000 genomes]
rs11057224	0.89[ASN][1000 genomes]
rs1109559	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1109560	0.88[ASN][1000 genomes]
rs11610710	0.82[ASN][1000 genomes]
rs1568427	0.82[ASN][1000 genomes]
rs1568428	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1611973	0.82[AFR][1000 genomes]
rs1616484	0.83[AFR][1000 genomes]
rs1626703	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1716178	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1716184	0.82[AFR][1000 genomes]
rs1727286	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1727293	0.82[AFR][1000 genomes]
rs1727295	0.82[AFR][1000 genomes]
rs1727301	0.80[ASN][1000 genomes]
rs1727305	0.82[AFR][1000 genomes]
rs1727312	0.82[AFR][1000 genomes]
rs1790088	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1790096	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1790104	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1790121	0.82[AFR][1000 genomes]
rs1790122	0.82[AFR][1000 genomes]
rs1790129	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1790134	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1879379	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2030401	0.88[ASN][1000 genomes]
rs2090764	0.80[ASN][1000 genomes]
rs2271976	0.89[ASN][1000 genomes]
rs2280424	0.83[ASN][1000 genomes]
rs2337631	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2682427	0.80[ASN][1000 genomes]
rs34841857	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4474478	0.84[ASN][1000 genomes]
rs4474479	0.84[ASN][1000 genomes]
rs4553407	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4594040	0.84[ASN][1000 genomes]
rs61519741	0.83[ASN][1000 genomes]
rs61953394	0.89[ASN][1000 genomes]
rs7137286	0.83[ASN][1000 genomes]
rs7139321	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7312955	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs73231928	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	esv1836043	chr12:123709409-123822503	Weak transcription Flanking Active TSS Strong transcription Enhancers 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
rs2337630	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs2337630	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs2337630	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs2337630	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs2337630	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs2337630	ENSG00000130921	cis	multi-tissue	Pritchard
rs2337630	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123718800-123733800	Weak transcription	Aorta	Aorta
2	chr12:123718800-123739600	Weak transcription	Fetal Kidney	kidney
3	chr12:123719000-123735000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr12:123719200-123735200	Weak transcription	Ovary	ovary
5	chr12:123719600-123734200	Weak transcription	Colonic Mucosa	Colon
6	chr12:123719600-123738400	Weak transcription	NH-A	brain
7	chr12:123719800-123733600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr12:123719800-123733600	Weak transcription	Spleen	Spleen
9	chr12:123719800-123733800	Weak transcription	Fetal Intestine Large	intestine
10	chr12:123720000-123736000	Weak transcription	Gastric	stomach
11	chr12:123720000-123738000	Weak transcription	Small Intestine	intestine
12	chr12:123720200-123735200	Weak transcription	Pancreas	Pancrea
13	chr12:123721000-123733800	Weak transcription	Lung	lung
14	chr12:123721600-123735200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr12:123722800-123733600	Weak transcription	Osteobl	bone
16	chr12:123723400-123735000	Weak transcription	Stomach Mucosa	stomach
17	chr12:123724600-123735200	Weak transcription	Placenta	Placenta
18	chr12:123725200-123738000	Weak transcription	HSMM	muscle
19	chr12:123725800-123746400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr12:123726600-123735200	Weak transcription	Fetal Muscle Trunk	muscle
21	chr12:123727000-123735000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr12:123727200-123735000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr12:123727200-123735000	Weak transcription	Brain Hippocampus Middle	brain
24	chr12:123727200-123735000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr12:123727200-123735200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr12:123727400-123733800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr12:123727400-123734800	Weak transcription	Hela-S3	cervix
28	chr12:123727400-123735000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr12:123727400-123735000	Weak transcription	Brain Anterior Caudate	brain
30	chr12:123727400-123735000	Weak transcription	Brain Substantia Nigra	brain
31	chr12:123727400-123735000	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr12:123727400-123735200	Weak transcription	Primary hematopoietic stem cells	blood
33	chr12:123727400-123735200	Weak transcription	Brain Angular Gyrus	brain
34	chr12:123727400-123735200	Weak transcription	Duodenum Mucosa	Duodenum
35	chr12:123727400-123735200	Weak transcription	Fetal Brain Male	brain
36	chr12:123727400-123735400	Weak transcription	Right Atrium	heart
37	chr12:123727400-123736000	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr12:123727400-123738000	Weak transcription	NHDF-Ad	bronchial
39	chr12:123727400-123738200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr12:123727600-123733200	Weak transcription	A549	lung
41	chr12:123727600-123735000	Weak transcription	Left Ventricle	heart
42	chr12:123727600-123735000	Weak transcription	HepG2	liver
43	chr12:123727600-123735200	Weak transcription	Adipose Nuclei	Adipose
44	chr12:123727600-123735200	Weak transcription	Brain Cingulate Gyrus	brain
45	chr12:123727600-123735200	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr12:123727600-123736400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr12:123727600-123738000	Weak transcription	Rectal Smooth Muscle	rectum
48	chr12:123727600-123738000	Weak transcription	HUVEC	blood vessel
49	chr12:123727600-123739200	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr12:123727800-123734200	Weak transcription	Skeletal Muscle Female	skeletal muscle

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