Variant report

Variant	rs2896888
Chromosome Location	chr2:127965811-127965812
allele	A/C
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	chr2:127965783-127966282	H1-hESC	embryonic stem cell:	n/a	n/a
2	TEAD4	chr2:127965769-127966308	ECC-1	luminal epithelium:	n/a	n/a
3	CTCF	chr2:127965680-127965830	HEK293	kidney:	n/a	n/a
4	TCF12	chr2:127965733-127966403	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:127965809..127968370-chr2:127982231..127984174,2	K562	blood:

Variant related genes	Relation type
CYP27C1	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12463909	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12465955	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12469035	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12623948	0.82[EUR][1000 genomes]
rs1566822	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2174270	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35328149	0.82[EUR][1000 genomes]
rs3902960	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4150407	0.85[EUR][1000 genomes]
rs4560059	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4580338	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4662710	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4662711	0.82[EUR][1000 genomes]
rs4662712	0.82[EUR][1000 genomes]
rs4662717	0.87[EUR][1000 genomes]
rs55905117	0.82[EUR][1000 genomes]
rs58475809	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6430931	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6712213	0.82[EUR][1000 genomes]
rs6712446	0.82[EUR][1000 genomes]
rs6712551	0.82[EUR][1000 genomes]
rs71414745	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7585198	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7591760	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9636235	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9636236	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[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	nsv1006112	chr2:127830117-128032546	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	esv2757832	chr2:127830943-128006514	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	esv2759090	chr2:127830943-128006514	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1011378	chr2:127841930-128020546	Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv999809	chr2:127841930-128032546	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1010669	chr2:127848860-128032546	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv1003599	chr2:127871183-128059407	Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv535920	chr2:127871183-128059407	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv961678	chr2:127961305-127979990	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	esv3331416	chr2:127962771-127980988	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2896888	AC068282.3	cis	Whole Blood	GTEx

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:127948800-127973400	Weak transcription	HMEC	breast
2	chr2:127952200-127975200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:127956400-127975800	Weak transcription	Fetal Kidney	kidney
4	chr2:127965400-127967000	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr2:127965600-127966000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr2:127965600-127966000	Enhancers	Muscle Satellite Cultured Cells	--
7	chr2:127965600-127966000	ZNF genes & repeats	Fetal Muscle Leg	muscle
8	chr2:127965600-127966400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
9	chr2:127965600-127966400	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr2:127965600-127966600	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr2:127965600-127966600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr2:127965600-127966600	Enhancers	Hela-S3	cervix
13	chr2:127965600-127966600	Enhancers	HSMM	muscle
14	chr2:127965600-127966800	Enhancers	H1 Cell Line	embryonic stem cell
15	chr2:127965600-127966800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr2:127965600-127966800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:127965600-127967000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:127965600-127967200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr2:127965800-127966000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
20	chr2:127965800-127966000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
21	chr2:127965800-127966000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
22	chr2:127965800-127966000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
23	chr2:127965800-127966200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:127965800-127966200	Enhancers	Fetal Lung	lung
25	chr2:127965800-127966400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr2:127965800-127966400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr2:127965800-127966400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:127965800-127966400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr2:127965800-127966600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:127965800-127966600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr2:127965800-127966600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr2:127965800-127966600	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr2:127965800-127966600	Enhancers	NHEK	skin
34	chr2:127965800-127966800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr2:127965800-127966800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr2:127965800-127966800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr2:127965800-127966800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:127965800-127966800	Enhancers	H9 Cell Line	embryonic stem cell
39	chr2:127965800-127966800	Enhancers	Esophagus	oesophagus
40	chr2:127965800-127966800	Enhancers	Placenta	Placenta
41	chr2:127965800-127967200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr2:127965800-127967200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr2:127965800-127967400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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