Variant report

Variant	rs1244872
Chromosome Location	chr12:65074345-65074346
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:65007806..65009395-chr12:65072726..65075432,2	MCF-7	breast:
2	chr12:65015837..65020171-chr12:65071764..65075735,5	MCF-7	breast:
3	chr12:65064246..65067121-chr12:65074124..65076207,3	K562	blood:
4	chr12:64798134..64800228-chr12:65072624..65075360,2	MCF-7	breast:
5	chr12:65071734..65074838-chr12:65083895..65087734,4	MCF-7	breast:
6	chr12:65002605..65004429-chr12:65071938..65074362,2	K562	blood:
7	chr12:65001203..65007582-chr12:65070748..65075652,10	MCF-7	breast:
8	chr12:65073563..65075604-chr12:65090075..65092190,3	MCF-7	breast:
9	chr12:65040502..65042059-chr12:65074229..65075840,2	MCF-7	breast:
10	chr12:65018029..65021346-chr12:65072247..65076410,6	MCF-7	breast:
11	chr12:65072722..65075110-chr12:65174388..65176087,2	MCF-7	breast:
12	chr12:65073323..65075797-chr12:65077372..65079298,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000153179	Chromatin interaction
ENSG00000184575	Chromatin interaction
ENSG00000256670	Chromatin interaction
ENSG00000207546	Chromatin interaction
ENSG00000268028	Chromatin interaction
ENSG00000111490	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10748011	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11175496	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1147097	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1147104	0.86[EUR][1000 genomes]
rs1147106	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1244870	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1244871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1244881	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1245170	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1261879	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1264239	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1270430	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1690261	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1716495	0.82[AMR][1000 genomes]
rs1716497	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1716518	1.00[CEU][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1795614	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1795617	0.82[EUR][1000 genomes]
rs1797690	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1797699	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2682713	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2682717	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2682721	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4264239	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs572046	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs577303	0.91[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7307999	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7308397	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	nsv899209	chr12:65068686-65184236	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:65064000-65076000	Enhancers	Fetal Thymus	thymus
2	chr12:65064000-65078200	Enhancers	Primary B cells from peripheral blood	blood
3	chr12:65066000-65078600	Enhancers	Spleen	Spleen
4	chr12:65067000-65075000	Weak transcription	Ovary	ovary
5	chr12:65067400-65076800	Weak transcription	Brain Angular Gyrus	brain
6	chr12:65068000-65074800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr12:65068000-65075800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr12:65068000-65076800	Weak transcription	Brain Germinal Matrix	brain
9	chr12:65068400-65087200	Weak transcription	Liver	Liver
10	chr12:65068600-65074800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr12:65068600-65075200	Weak transcription	Gastric	stomach
12	chr12:65068600-65076600	Weak transcription	Fetal Kidney	kidney
13	chr12:65068600-65076800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr12:65068600-65078000	Weak transcription	Dnd41	blood
15	chr12:65068600-65079400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr12:65069400-65077000	Weak transcription	Psoas Muscle	Psoas
17	chr12:65069800-65074800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr12:65070000-65074800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr12:65070000-65085200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr12:65070000-65092400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr12:65070600-65075200	Enhancers	Primary hematopoietic stem cells	blood
22	chr12:65070600-65075800	Enhancers	Primary B cells from cord blood	blood
23	chr12:65070600-65076600	Enhancers	Fetal Heart	heart
24	chr12:65070800-65076000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
25	chr12:65070800-65079600	Enhancers	Colon Smooth Muscle	Colon
26	chr12:65071600-65074800	Enhancers	Primary T cells from cord blood	blood
27	chr12:65072000-65074400	Enhancers	Lung	lung
28	chr12:65072000-65074400	Flanking Active TSS	A549	lung
29	chr12:65072000-65074800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr12:65072000-65077400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr12:65072200-65075600	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr12:65072200-65077200	Enhancers	Left Ventricle	heart
33	chr12:65072200-65081600	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr12:65072400-65074600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr12:65072400-65074800	Enhancers	Monocytes-CD14+_RO01746	blood
36	chr12:65072400-65076000	Enhancers	Stomach Mucosa	stomach
37	chr12:65072600-65074400	Flanking Active TSS	Hela-S3	cervix
38	chr12:65072600-65075400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr12:65072600-65075600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr12:65072600-65076400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr12:65072600-65078400	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr12:65072800-65076400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr12:65073200-65074400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr12:65073200-65074400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr12:65073200-65074400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
46	chr12:65073200-65074400	Enhancers	Fetal Muscle Trunk	muscle
47	chr12:65073200-65074400	Flanking Active TSS	NHEK	skin
48	chr12:65073200-65075400	Enhancers	Fetal Intestine Small	intestine
49	chr12:65073200-65075600	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr12:65073200-65075800	Enhancers	Placenta	Placenta

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