Variant report

Variant	rs4672096
Chromosome Location	chr2:56413345-56413346
allele	G/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	POLR2A	chr2:56413332-56413368	HUVEC	blood vessel:	n/a	n/a
2	REST	chr2:56412224-56413569	H1-neurons	neurons:	n/a	chr2:56413204-56413224 chr2:56412496-56412509
3	POLR2A	chr2:56412167-56413464	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr2:56412138-56413547	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr2:56410584-56413719	HUVEC	blood vessel:	n/a	n/a

Variant related genes	Relation type
ENSG00000233251	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11674133	0.94[ASN][1000 genomes]
rs13034898	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1814276	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2216328	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[ASN][1000 genomes]
rs4671275	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs6545561	0.83[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs6733298	1.00[MEX][hapmap];0.86[TSI][hapmap]
rs6735241	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6756156	0.81[MEX][hapmap]
rs7419516	1.00[CHB][hapmap];0.91[CHD][hapmap];0.84[ASN][1000 genomes]
rs7576331	0.86[ASN][1000 genomes]
rs960489	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs960490	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757799	chr2:56178439-56472394	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	esv2759051	chr2:56178439-56472394	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
3	nsv874162	chr2:56255832-56480571	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv874169	chr2:56383762-56473480	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv2762648	chr2:56386656-56422448	Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:56410600-56413400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr2:56410600-56413400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr2:56410600-56413400	Active TSS	Brain Hippocampus Middle	brain
4	chr2:56410600-56413400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:56410600-56413600	Active TSS	Psoas Muscle	Psoas
6	chr2:56410600-56413600	Active TSS	Right Atrium	heart
7	chr2:56410800-56413400	Active TSS	Left Ventricle	heart
8	chr2:56410800-56413600	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr2:56412200-56413400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
10	chr2:56412200-56413400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
11	chr2:56412200-56413400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
12	chr2:56412200-56413600	Flanking Active TSS	Adipose Nuclei	Adipose
13	chr2:56412400-56413400	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr2:56412600-56413400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:56412600-56413400	Flanking Active TSS	Brain Anterior Caudate	brain
16	chr2:56412600-56413400	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
17	chr2:56413000-56413400	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
18	chr2:56413000-56413400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
19	chr2:56413000-56413400	Bivalent Enhancer	Fetal Intestine Small	intestine
20	chr2:56413000-56413400	Bivalent Enhancer	Fetal Kidney	kidney
21	chr2:56413000-56413400	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
22	chr2:56413000-56413400	Flanking Active TSS	HSMMtube	muscle
23	chr2:56413000-56413600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
24	chr2:56413000-56413600	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
25	chr2:56413000-56413600	Transcr. at gene 5' and 3'	HSMM	muscle
26	chr2:56413000-56413600	Flanking Active TSS	HUVEC	blood vessel
27	chr2:56413200-56413400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
28	chr2:56413200-56413400	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
29	chr2:56413200-56413400	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr2:56413200-56413400	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:56413200-56413400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
32	chr2:56413200-56413400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
33	chr2:56413200-56413400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
34	chr2:56413200-56413400	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr2:56413200-56413400	Flanking Active TSS	Brain Angular Gyrus	brain
36	chr2:56413200-56413400	Flanking Active TSS	Brain Cingulate Gyrus	brain
37	chr2:56413200-56413400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
38	chr2:56413200-56413400	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
39	chr2:56413200-56413400	Bivalent Enhancer	Fetal Stomach	stomach
40	chr2:56413200-56413600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
41	chr2:56413200-56413600	Bivalent Enhancer	Fetal Brain Male	brain
42	chr2:56413200-56413600	Enhancers	Fetal Heart	heart
43	chr2:56413200-56413600	Enhancers	Lung	lung
44	chr2:56413200-56413800	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr2:56413200-56419600	Weak transcription	Placenta	Placenta
46	chr2:56413200-56419800	Weak transcription	Right Ventricle	heart

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