Variant report

Variant	rs2272061
Chromosome Location	chr2:169746215-169746216
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	HNF4G	chr2:169746112-169746524	HepG2	liver:	n/a	chr2:169746292-169746307
2	SIN3A	chr2:169746211-169747310	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr2:169746202-169747501	PBDE	blood:	n/a	n/a
4	ZNF143	chr2:169746199-169746270	GM12878	blood:	n/a	n/a
5	E2F4	chr2:169745245-169748180	MCF10A-Er-Src	breast:	n/a	chr2:169746952-169746964 chr2:169746990-169746999 chr2:169746951-169746962
6	HCFC1	chr2:169746145-169747542	K562	blood:	n/a	n/a
7	NR2F2	chr2:169746125-169747634	K562	blood:	n/a	chr2:169747212-169747227
8	HNF4A	chr2:169746190-169746436	HepG2	liver:	n/a	chr2:169746292-169746307
9	POLR2A	chr2:169746191-169747138	GM19099	blood:	n/a	n/a
10	TEAD4	chr2:169746049-169747643	K562	blood:	n/a	n/a
11	TBP	chr2:169746164-169747276	K562	blood:	n/a	n/a
12	POLR2A	chr2:169745915-169747127	K562	blood:	n/a	n/a
13	POLR2A	chr2:169746203-169747084	HepG2	liver:	n/a	n/a
14	CBX3	chr2:169746085-169747364	K562	blood:	n/a	chr2:169746470-169746481
15	MYC	chr2:169746081-169747429	K562	blood:	n/a	n/a
16	MYBL2	chr2:169746090-169747337	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
SPC25	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11893114	1.00[JPT][hapmap]
rs1522018	1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs16823013	1.00[JPT][hapmap]
rs16856030	1.00[JPT][hapmap]
rs16856059	1.00[JPT][hapmap]
rs16856065	1.00[JPT][hapmap];1.00[AMR][1000 genomes]
rs2272060	1.00[ASN][1000 genomes]
rs2272062	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3814384	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6749007	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv583599	chr2:169664227-169903096	Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv875381	chr2:169686559-169749841	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv3417763	chr2:169744606-169746654	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:169717000-169746400	Weak transcription	Primary B cells from cord blood	blood
2	chr2:169731800-169746600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:169739400-169746400	Weak transcription	Primary T cells from cord blood	blood
4	chr2:169744800-169746400	Weak transcription	Pancreas	Pancrea
5	chr2:169744800-169746400	Weak transcription	Spleen	Spleen
6	chr2:169745600-169746400	Flanking Active TSS	Dnd41	blood
7	chr2:169745600-169746400	Transcr. at gene 5' and 3'	K562	blood
8	chr2:169745800-169746400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr2:169745800-169746400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:169745800-169746400	Flanking Active TSS	Thymus	Thymus
11	chr2:169745800-169746400	Flanking Active TSS	Hela-S3	cervix
12	chr2:169745800-169746400	Flanking Active TSS	HMEC	breast
13	chr2:169745800-169746600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr2:169745800-169746600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr2:169745800-169746600	Flanking Active TSS	Fetal Heart	heart
16	chr2:169745800-169746600	Flanking Active TSS	NHEK	skin
17	chr2:169745800-169746800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:169745800-169746800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
19	chr2:169745800-169746800	Flanking Active TSS	HUVEC	blood vessel
20	chr2:169745800-169747200	Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr2:169745800-169747200	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr2:169745800-169747200	Active TSS	iPS-18 Cell Line	embryonic stem cell
23	chr2:169745800-169747200	Active TSS	HSMM	muscle
24	chr2:169745800-169747400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr2:169745800-169747400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr2:169745800-169747400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr2:169745800-169747400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr2:169745800-169747400	Active TSS	Fetal Kidney	kidney
29	chr2:169745800-169747600	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr2:169745800-169747600	Active TSS	A549	lung
31	chr2:169746000-169746400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr2:169746000-169746400	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr2:169746000-169746400	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr2:169746000-169746400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr2:169746000-169746400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr2:169746000-169746400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr2:169746000-169746400	Enhancers	Placenta Amnion	Placenta Amnion
38	chr2:169746000-169746400	Flanking Active TSS	NHLF	lung
39	chr2:169746000-169746600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr2:169746000-169746600	Flanking Active TSS	Fetal Lung	lung
41	chr2:169746000-169746600	Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr2:169746000-169746800	Flanking Active TSS	Primary hematopoietic stem cells	blood
43	chr2:169746000-169746800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr2:169746000-169746800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr2:169746000-169746800	Flanking Active TSS	Duodenum Mucosa	Duodenum
46	chr2:169746000-169746800	Flanking Active TSS	Fetal Stomach	stomach
47	chr2:169746000-169747000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr2:169746000-169747200	Active TSS	iPS-20b Cell Line	embryonic stem cell
49	chr2:169746000-169747200	Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr2:169746000-169747400	Active TSS	H1 Cell Line	embryonic stem cell

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