Variant report

Variant	rs7592947
Chromosome Location	chr2:113523130-113523131
allele	A/G
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	WRNIP1	chr2:113522894-113523221	GM12878	blood:	n/a	n/a
2	MXI1	chr2:113520973-113523230	SK-N-SH	brain:	n/a	n/a
3	EP300	chr2:113523106-113523180	GM12878	blood:	n/a	n/a
4	MAZ	chr2:113521419-113523163	IMR90	lung:	n/a	chr2:113521952-113521962
5	E2F4	chr2:113520746-113523185	MCF10A-Er-Src	breast:	n/a	chr2:113522294-113522306 chr2:113521741-113521750
6	POLR2A	chr2:113521619-113523133	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:113485399..113487990-chr2:113522114..113523918,2	K562	blood:
2	chr2:113403176..113405002-chr2:113522178..113523741,2	K562	blood:
3	chr2:113512694..113515330-chr2:113521707..113523749,2	K562	blood:
4	chr2:113402414..113404382-chr2:113520815..113523652,2	MCF-7	breast:
5	chr2:113519458..113523816-chr2:113539890..113544534,4	K562	blood:

Variant related genes	Relation type
CKAP2L	TF binding region
ENSG00000144136	Chromatin interaction
ENSG00000115008	Chromatin interaction
ENSG00000169607	Chromatin interaction
ENSG00000237753	Chromatin interaction
ENSG00000144130	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11123150	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1304037	0.94[ASW][hapmap];0.82[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs13417956	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs1800587	0.80[ASW][hapmap]
rs1878319	0.86[YRI][hapmap]
rs1878320	0.83[YRI][hapmap]
rs1878321	0.83[YRI][hapmap]
rs4848299	0.91[AFR][1000 genomes]
rs4848300	0.94[ASW][hapmap];0.82[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs6542090	0.91[AFR][1000 genomes]
rs6542091	0.88[AFR][1000 genomes]
rs6542092	0.89[AFR][1000 genomes]
rs6542093	0.89[AFR][1000 genomes]
rs6542094	0.87[AFR][1000 genomes]
rs7570215	0.89[AFR][1000 genomes]
rs7604926	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428724	chr2:113376894-113555421	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv1010106	chr2:113394981-113556071	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7592947	PAX8	cis	cerebellum	SCAN
rs7592947	IL1B	cis	parietal	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113520800-113523200	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr2:113520800-113523200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:113520800-113523200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:113521200-113523200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:113521400-113523200	Active TSS	Muscle Satellite Cultured Cells	--
6	chr2:113521400-113523200	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr2:113521400-113523200	Active TSS	Fetal Brain Female	brain
8	chr2:113521400-113523200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr2:113521600-113523200	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr2:113521600-113523200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr2:113521800-113523200	Active TSS	Fetal Lung	lung
12	chr2:113522000-113523200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr2:113522000-113523200	Active TSS	Aorta	Aorta
14	chr2:113522000-113523200	Active TSS	Ovary	ovary
15	chr2:113522000-113523200	Active TSS	Rectal Smooth Muscle	rectum
16	chr2:113522000-113523200	Active TSS	Spleen	Spleen
17	chr2:113522600-113523200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
18	chr2:113522600-113523200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr2:113522600-113523200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
20	chr2:113522600-113523200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:113522600-113523200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr2:113522600-113523200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr2:113522600-113523200	Flanking Active TSS	Duodenum Mucosa	Duodenum
24	chr2:113522600-113523200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr2:113522600-113523200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
26	chr2:113522600-113523200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
27	chr2:113522600-113523200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr2:113522600-113523200	Flanking Active TSS	Dnd41	blood
29	chr2:113522600-113523200	Flanking Active TSS	Osteobl	bone
30	chr2:113522800-113523200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:113522800-113523200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr2:113522800-113523200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr2:113522800-113523200	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr2:113522800-113523200	Enhancers	Primary B cells from peripheral blood	blood
35	chr2:113522800-113523200	Enhancers	Primary T cells fromperipheralblood	blood
36	chr2:113522800-113523200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr2:113522800-113523200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr2:113522800-113523200	Enhancers	Liver	Liver
39	chr2:113522800-113523200	Flanking Active TSS	Brain Germinal Matrix	brain
40	chr2:113522800-113523200	Flanking Active TSS	Brain Hippocampus Middle	brain
41	chr2:113522800-113523200	Flanking Active TSS	Colon Smooth Muscle	Colon
42	chr2:113522800-113523200	Flanking Active TSS	Fetal Heart	heart
43	chr2:113522800-113523200	Flanking Active TSS	Stomach Smooth Muscle	stomach
44	chr2:113522800-113523200	Flanking Active TSS	A549	lung
45	chr2:113522800-113523200	Flanking Active TSS	GM12878-XiMat	blood
46	chr2:113522800-113523200	Flanking Active TSS	Hela-S3	cervix
47	chr2:113522800-113523200	Flanking Active TSS	HepG2	liver
48	chr2:113522800-113523200	Flanking Active TSS	HMEC	breast
49	chr2:113522800-113523200	Flanking Active TSS	K562	blood
50	chr2:113522800-113523200	Flanking Active TSS	NHEK	skin

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