Variant report

Variant	rs2682721
Chromosome Location	chr12:65025687-65025688
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:65024701..65026859-chr12:65028365..65030970,2	MCF-7	breast:
2	chr12:65002843..65006051-chr12:65023812..65028025,5	MCF-7	breast:
3	chr12:65023053..65026165-chr12:65027701..65030902,3	K562	blood:
4	chr12:65024223..65026567-chr12:65034378..65036625,2	K562	blood:
5	chr12:65019590..65021389-chr12:65024467..65026055,3	K562	blood:
6	chr12:65017967..65023597-chr12:65023649..65027949,8	MCF-7	breast:
7	chr12:65006929..65009756-chr12:65024584..65028826,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256670	Chromatin interaction
ENSG00000225195	Chromatin interaction
ENSG00000153179	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10748011	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11175496	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1147097	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1147104	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1147106	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1244870	0.81[ASN][1000 genomes]
rs1244871	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1244872	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1244881	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1245170	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1245182	0.92[YRI][hapmap]
rs1261879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1264239	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1270430	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1520766	0.85[EUR][1000 genomes]
rs1690261	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1716497	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1716518	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1795614	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1795617	0.93[EUR][1000 genomes]
rs1797690	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1797699	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2682713	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2682717	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4264239	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs572046	0.80[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs577303	0.91[CEU][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7307999	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7308397	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832443	chr12:64878856-65057265	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv832444	chr12:64981484-65168472	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv559203	chr12:65002969-65199922	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1045216	chr12:65009102-65176894	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv541513	chr12:65009102-65176894	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv469457	chr12:65009243-65195977	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv559204	chr12:65009243-65195977	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv438218	chr12:65017844-65037483	Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:65006800-65031800	Weak transcription	Dnd41	blood
2	chr12:65018400-65029200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr12:65018600-65035000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:65019600-65027800	Weak transcription	Pancreas	Pancrea
5	chr12:65019800-65025800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:65019800-65025800	Weak transcription	Fetal Lung	lung
7	chr12:65019800-65025800	Weak transcription	Psoas Muscle	Psoas
8	chr12:65019800-65026200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr12:65019800-65026400	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr12:65019800-65026600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr12:65019800-65028400	Weak transcription	Colonic Mucosa	Colon
12	chr12:65019800-65028600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr12:65019800-65029200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr12:65019800-65030600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr12:65019800-65047400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr12:65020200-65026000	Weak transcription	Fetal Thymus	thymus
17	chr12:65020200-65026200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr12:65020200-65026400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr12:65020400-65026400	Weak transcription	Primary hematopoietic stem cells	blood
20	chr12:65020400-65027400	Weak transcription	Fetal Intestine Large	intestine
21	chr12:65020600-65028200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr12:65020800-65027800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr12:65021200-65025800	Weak transcription	HepG2	liver
24	chr12:65021200-65026400	Weak transcription	K562	blood
25	chr12:65021200-65031200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr12:65021400-65029600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
27	chr12:65021400-65043400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr12:65021600-65026200	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr12:65021600-65029400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
30	chr12:65021600-65030600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr12:65021800-65026800	Weak transcription	Hela-S3	cervix
32	chr12:65021800-65027200	Weak transcription	Small Intestine	intestine
33	chr12:65021800-65027600	Weak transcription	NHEK	skin
34	chr12:65021800-65037000	Weak transcription	Adipose Nuclei	Adipose
35	chr12:65021800-65038000	Weak transcription	Ovary	ovary
36	chr12:65022000-65027600	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr12:65022000-65027800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr12:65022200-65026400	Strong transcription	Fetal Stomach	stomach
39	chr12:65022200-65027800	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr12:65022200-65029200	Genic enhancers	Primary T cells fromperipheralblood	blood
41	chr12:65022400-65026200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr12:65022400-65026200	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr12:65022400-65026200	Weak transcription	Stomach Mucosa	stomach
44	chr12:65022400-65027600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr12:65022400-65029200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr12:65022400-65039600	Weak transcription	Osteobl	bone
47	chr12:65023000-65027400	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr12:65023000-65027600	Genic enhancers	Primary B cells from peripheral blood	blood
49	chr12:65023600-65029000	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr12:65023600-65029800	Genic enhancers	Primary T cells from cord blood	blood

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