Variant report

Variant	rs13306264
Chromosome Location	chr2:189838800-189838801
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	TEAD4	chr2:189838195-189838836	SK-N-SH	brain:	n/a	n/a
2	NFIC	chr2:189838074-189839541	SK-N-SH	brain:	n/a	chr2:189838668-189838696
3	MAX	chr2:189838795-189839356	SK-N-SH	brain:	n/a	n/a
4	PBX3	chr2:189838215-189839417	SK-N-SH	brain:	n/a	n/a
5	TCF12	chr2:189838100-189839388	SK-N-SH	brain:	n/a	n/a
6	GATA3	chr2:189837699-189839505	SK-N-SH	brain:	n/a	n/a
7	GATA3	chr2:189837736-189839665	SK-N-SH	brain:	n/a	chr2:189839506-189839513 chr2:189839506-189839513 chr2:189839506-189839513
8	EP300	chr2:189838096-189839403	SK-N-SH	brain:	n/a	chr2:189838332-189838346 chr2:189838964-189838978 chr2:189838152-189838159 chr2:189838781-189838795
9	TCF12	chr2:189838087-189839738	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr2:189838224-189842514	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:189652355..189655667-chr2:189836980..189839231,3	MCF-7	breast:

Variant related genes	Relation type
COL3A1	TF binding region
MIR1245A	TF binding region
ENSG00000174325	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11675562	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs17357358	0.83[ASN][1000 genomes]
rs17357387	0.83[ASN][1000 genomes]
rs17357408	0.83[ASN][1000 genomes]
rs4308073	0.94[ASN][1000 genomes]
rs56284022	0.94[ASN][1000 genomes]
rs6414122	1.00[JPT][hapmap]
rs67712818	0.80[ASN][1000 genomes]
rs72908672	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs72908674	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs72908683	0.83[ASN][1000 genomes]
rs72910726	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs72910727	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs72910734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs72910737	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][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	nsv834490	chr2:189703550-189840963	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv584056	chr2:189796272-189841052	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv459992	chr2:189796272-189855943	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
4	nsv584057	chr2:189796272-189855943	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
5	nsv875609	chr2:189796272-189862097	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv875610	chr2:189796272-189904674	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv584058	chr2:189799499-189855943	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
8	esv1791841	chr2:189811074-189864582	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189830800-189839000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr2:189834200-189838800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:189834200-189842800	Weak transcription	A549	lung
4	chr2:189835400-189838800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr2:189835400-189839200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:189836200-189839000	Weak transcription	Esophagus	oesophagus
7	chr2:189836800-189838800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr2:189837400-189844000	Active TSS	NHDF-Ad	bronchial
9	chr2:189837800-189838800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:189837800-189839200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr2:189837800-189842800	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr2:189837800-189844800	Active TSS	Stomach Smooth Muscle	stomach
13	chr2:189838000-189844600	Active TSS	Right Atrium	heart
14	chr2:189838000-189844800	Active TSS	Adipose Nuclei	Adipose
15	chr2:189838000-189844800	Active TSS	NHLF	lung
16	chr2:189838200-189839000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr2:189838200-189843000	Active TSS	Fetal Lung	lung
18	chr2:189838200-189844800	Active TSS	Fetal Stomach	stomach
19	chr2:189838200-189846000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr2:189838200-189849400	Active TSS	Fetal Muscle Leg	muscle
21	chr2:189838400-189839000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
22	chr2:189838400-189839000	Flanking Active TSS	Osteobl	bone
23	chr2:189838400-189842200	Active TSS	NH-A	brain
24	chr2:189838400-189843400	Active TSS	Fetal Intestine Small	intestine
25	chr2:189838400-189844400	Active TSS	Fetal Intestine Large	intestine
26	chr2:189838400-189844600	Active TSS	Fetal Kidney	kidney
27	chr2:189838400-189844600	Active TSS	Rectal Mucosa Donor 29	rectum
28	chr2:189838400-189844800	Active TSS	Fetal Muscle Trunk	muscle
29	chr2:189838400-189845000	Active TSS	HSMMtube	muscle
30	chr2:189838600-189839000	Enhancers	Small Intestine	intestine
31	chr2:189838600-189839200	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:189838600-189839400	Enhancers	HUVEC	blood vessel
33	chr2:189838600-189843000	Active TSS	Aorta	Aorta
34	chr2:189838600-189843000	Active TSS	HSMM	muscle
35	chr2:189838600-189843600	Active TSS	Skeletal Muscle Male	skeletal muscle
36	chr2:189838600-189844600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:189838600-189844600	Active TSS	Rectal Smooth Muscle	rectum
38	chr2:189838600-189844800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr2:189838600-189844800	Active TSS	Colon Smooth Muscle	Colon
40	chr2:189838600-189844800	Active TSS	Ovary	ovary
41	chr2:189838800-189839000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr2:189838800-189839400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr2:189838800-189842400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr2:189838800-189843000	Active TSS	Placenta	Placenta
45	chr2:189838800-189843600	Active TSS	Placenta Amnion	Placenta Amnion
46	chr2:189838800-189843600	Active TSS	Rectal Mucosa Donor 31	rectum
47	chr2:189838800-189844000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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