Variant report

Variant	rs12296535
Chromosome Location	chr12:47054654-47054655
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:46972689..46974788-chr12:47053934..47056734,2	MCF-7	breast:
2	chr12:47054064..47055917-chr12:47057458..47059164,2	K562	blood:
3	chr12:46756339..46758839-chr12:47053863..47055501,2	MCF-7	breast:
4	chr12:46775880..46778772-chr12:47053263..47055840,3	MCF-7	breast:
5	chr12:46759450..46767729-chr12:47050364..47062392,28	MCF-7	breast:
6	chr12:46886016..46887722-chr12:47054283..47056459,2	MCF-7	breast:
7	chr12:46760654..46769647-chr12:47051646..47061944,32	MCF-7	breast:
8	chr12:46757823..46760512-chr12:47053505..47055776,2	K562	blood:
9	chr12:46887516..46889882-chr12:47054053..47056770,2	MCF-7	breast:
10	chr12:47053397..47056382-chr12:47060303..47062102,2	MCF-7	breast:
11	chr12:46762091..46766718-chr12:47051293..47055848,8	K562	blood:
12	chr12:46745913..46748762-chr12:47052132..47055018,2	K562	blood:
13	chr12:46764217..46768302-chr12:47052891..47055832,5	K562	blood:
14	chr12:46776215..46777851-chr12:47053337..47055678,2	K562	blood:
15	chr12:46754872..46757316-chr12:47052968..47055309,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000134294	Chromatin interaction
ENSG00000257261	Chromatin interaction
ENSG00000258096	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10467215	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs11183500	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs11183510	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs11183541	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1118657	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1118658	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11504533	0.90[ASN][1000 genomes]
rs12302091	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12303838	1.00[ASN][1000 genomes]
rs12306495	0.88[ASN][1000 genomes]
rs12307183	0.90[ASN][1000 genomes]
rs12311537	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12318364	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12321468	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12321960	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs17096998	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs1895088	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3935048	0.87[JPT][hapmap]
rs57964461	0.90[ASN][1000 genomes]
rs58190601	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60053128	0.88[ASN][1000 genomes]
rs60487001	0.86[ASN][1000 genomes]
rs61562961	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7313172	1.00[EUR][1000 genomes]
rs73293953	0.90[ASN][1000 genomes]
rs759702	1.00[ASN][1000 genomes]
rs759703	1.00[ASN][1000 genomes]
rs7953339	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs7967889	0.82[JPT][hapmap]
rs7980023	0.82[CHB][hapmap];0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
3	esv3416674	chr12:46988689-47178369	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv558783	chr12:46996632-47144856	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv1844378	chr12:47028797-47072016	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv1845143	chr12:47051076-47431496	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47042200-47054800	Weak transcription	Fetal Intestine Small	intestine
2	chr12:47046400-47069800	Weak transcription	Pancreas	Pancrea
3	chr12:47046800-47057000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:47050800-47055000	Enhancers	Muscle Satellite Cultured Cells	--
5	chr12:47050800-47056000	Enhancers	NHLF	lung
6	chr12:47051000-47055000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr12:47051000-47056200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr12:47051200-47055000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr12:47051400-47055600	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr12:47051400-47055800	Enhancers	Fetal Heart	heart
11	chr12:47051400-47055800	Enhancers	HSMM	muscle
12	chr12:47051400-47056200	Enhancers	HUVEC	blood vessel
13	chr12:47051400-47059800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr12:47051600-47055600	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr12:47051800-47055000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr12:47051800-47055400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr12:47051800-47056000	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr12:47051800-47056000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:47052200-47055000	Weak transcription	Placenta	Placenta
20	chr12:47052200-47055600	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr12:47052400-47055600	Enhancers	Primary T cells from cord blood	blood
22	chr12:47052600-47055400	Enhancers	Fetal Stomach	stomach
23	chr12:47052600-47056000	Enhancers	Primary hematopoietic stem cells	blood
24	chr12:47052800-47055200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr12:47052800-47055400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr12:47052800-47055400	Enhancers	Fetal Muscle Leg	muscle
27	chr12:47053000-47055000	Enhancers	Fetal Thymus	thymus
28	chr12:47053000-47055200	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr12:47053000-47055200	Enhancers	Small Intestine	intestine
30	chr12:47053000-47055800	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr12:47053200-47055000	Weak transcription	Brain Cingulate Gyrus	brain
32	chr12:47053200-47055200	Enhancers	GM12878-XiMat	blood
33	chr12:47053200-47055400	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr12:47053200-47055600	Enhancers	Primary B cells from peripheral blood	blood
35	chr12:47053200-47055800	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr12:47053400-47054800	Enhancers	Colon Smooth Muscle	Colon
37	chr12:47053400-47054800	Weak transcription	HSMMtube	muscle
38	chr12:47053400-47055000	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr12:47053400-47055200	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr12:47053400-47055400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr12:47053400-47055400	Enhancers	Adipose Nuclei	Adipose
42	chr12:47053400-47055400	Enhancers	Rectal Smooth Muscle	rectum
43	chr12:47053400-47055400	Enhancers	NHDF-Ad	bronchial
44	chr12:47053400-47055600	Enhancers	Fetal Lung	lung
45	chr12:47053400-47055800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr12:47053400-47058200	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr12:47053400-47058600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr12:47053400-47062400	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr12:47053600-47055600	Enhancers	Primary neutrophils fromperipheralblood	blood
50	chr12:47053600-47055600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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