Variant report

Variant	rs11613937
Chromosome Location	chr12:123520071-123520072
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	GATA3	chr12:123519422-123520088	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:123519868..123522613-chr12:123530102..123532042,2	K562	blood:
2	chr12:123519670..123521878-chr12:123527130..123529862,2	MCF-7	breast:

Variant related genes	Relation type
PITPNM2	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10773921	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10848428	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11608811	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12425009	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12425850	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1727307	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1790094	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1790106	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1790121	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1790122	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1984658	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28755851	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3741530	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3759115	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3897102	0.91[ASN][1000 genomes]
rs4148862	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4148863	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4275659	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55742290	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61955196	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61955214	0.90[ASN][1000 genomes]
rs7135296	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7296418	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7305511	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7957096	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs883562	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs884956	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs949143	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv899573	chr12:123312051-123528405	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	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
4	nsv899576	chr12:123335527-123528405	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv832532	chr12:123395927-123573137	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv832533	chr12:123395927-123589290	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	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
8	nsv455732	chr12:123427573-123574838	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer 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	37 gene(s)	inside rSNPs	diseases
9	nsv560492	chr12:123427573-123574838	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking 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	37 gene(s)	inside rSNPs	diseases
10	nsv560494	chr12:123478378-123560731	Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11613937	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs11613937	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs11613937	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs11613937	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs11613937	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs11613937	SBNO1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123470400-123526600	Weak transcription	Fetal Lung	lung
2	chr12:123490200-123528200	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr12:123491600-123526400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr12:123496000-123526400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr12:123497400-123528600	Weak transcription	Ovary	ovary
6	chr12:123497800-123526000	Weak transcription	Colon Smooth Muscle	Colon
7	chr12:123504200-123528000	Weak transcription	HMEC	breast
8	chr12:123504400-123540200	Weak transcription	Hela-S3	cervix
9	chr12:123507400-123526000	Genic enhancers	Fetal Thymus	thymus
10	chr12:123509800-123525600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr12:123509800-123530400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr12:123511400-123528200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr12:123515600-123521600	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr12:123516400-123527400	Weak transcription	Brain Hippocampus Middle	brain
15	chr12:123516600-123527800	Weak transcription	Stomach Mucosa	stomach
16	chr12:123517200-123521800	Enhancers	Primary hematopoietic stem cells	blood
17	chr12:123517400-123520600	Enhancers	K562	blood
18	chr12:123517800-123526800	Weak transcription	Fetal Heart	heart
19	chr12:123517800-123527200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr12:123518000-123526400	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr12:123518200-123527600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:123518200-123528000	Weak transcription	Brain Anterior Caudate	brain
23	chr12:123518200-123535600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr12:123518400-123527200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr12:123518400-123527200	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr12:123518400-123533600	Weak transcription	Aorta	Aorta
27	chr12:123518800-123520600	Weak transcription	Brain Germinal Matrix	brain
28	chr12:123518800-123526000	Weak transcription	Placenta	Placenta
29	chr12:123518800-123526400	Weak transcription	Fetal Muscle Leg	muscle
30	chr12:123518800-123527400	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr12:123518800-123528200	Weak transcription	Brain Substantia Nigra	brain
32	chr12:123518800-123540600	Weak transcription	HepG2	liver
33	chr12:123519000-123524400	Genic enhancers	Thymus	Thymus
34	chr12:123519000-123526200	Weak transcription	Duodenum Mucosa	Duodenum
35	chr12:123519000-123526400	Weak transcription	Pancreas	Pancrea
36	chr12:123519000-123526600	Weak transcription	Fetal Intestine Large	intestine
37	chr12:123519000-123527400	Weak transcription	Colonic Mucosa	Colon
38	chr12:123519000-123527400	Weak transcription	Spleen	Spleen
39	chr12:123519000-123527800	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr12:123519000-123528200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr12:123519000-123528200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr12:123519000-123540400	Weak transcription	Gastric	stomach
43	chr12:123519000-123543400	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr12:123519200-123520200	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr12:123519200-123521600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr12:123519200-123521600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr12:123519200-123524000	Weak transcription	Liver	Liver
48	chr12:123519200-123525800	Weak transcription	Fetal Intestine Small	intestine
49	chr12:123519200-123526400	Weak transcription	Lung	lung
50	chr12:123519200-123526600	Weak transcription	Right Ventricle	heart

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