Variant report

Variant	rs12296783
Chromosome Location	chr12:46878561-46878562
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:46876888..46879463-chr12:46886100..46887929,2	MCF-7	breast:
2	chr12:46765188..46768496-chr12:46877809..46880766,4	MCF-7	breast:
3	chr12:46870046..46873030-chr12:46878483..46880314,2	MCF-7	breast:
4	chr12:46868625..46870317-chr12:46878196..46880801,2	MCF-7	breast:
5	chr12:46776146..46779343-chr12:46878535..46880853,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ARID2-3	chr12:46878241-46878663	XLOC_009723

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

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10467215	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11183500	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183510	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11183512	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11183513	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11830086	1.00[EUR][1000 genomes]
rs11834444	1.00[EUR][1000 genomes]
rs12302091	0.81[ASN][1000 genomes]
rs12317179	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12317255	0.95[ASN][1000 genomes]
rs12321960	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17096996	1.00[EUR][1000 genomes]
rs17096998	0.91[ASN][1000 genomes]
rs2408578	1.00[EUR][1000 genomes]
rs34098443	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36010856	0.95[ASN][1000 genomes]
rs3935048	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55649919	1.00[EUR][1000 genomes]
rs58127062	0.92[ASN][1000 genomes]
rs58353248	0.92[ASN][1000 genomes]
rs58890669	0.95[ASN][1000 genomes]
rs59451063	1.00[EUR][1000 genomes]
rs59608605	0.95[ASN][1000 genomes]
rs60876255	1.00[EUR][1000 genomes]
rs61351787	1.00[EUR][1000 genomes]
rs7136748	1.00[EUR][1000 genomes]
rs7313172	0.92[ASN][1000 genomes]
rs73290315	0.95[ASN][1000 genomes]
rs74085404	1.00[EUR][1000 genomes]
rs74085421	1.00[EUR][1000 genomes]
rs74085432	1.00[EUR][1000 genomes]
rs74085442	1.00[EUR][1000 genomes]
rs74085444	1.00[EUR][1000 genomes]
rs74085447	1.00[EUR][1000 genomes]
rs7953339	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7967889	0.95[ASN][1000 genomes]
rs7975472	1.00[EUR][1000 genomes]
rs7980023	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1842882	chr12:46691487-47009428	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
2	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
3	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
4	esv3429861	chr12:46762813-46988789	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	145 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46844600-46886000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:46865400-46879200	Weak transcription	Right Ventricle	heart
3	chr12:46868000-46881200	Weak transcription	GM12878-XiMat	blood
4	chr12:46868000-46883200	Weak transcription	Fetal Heart	heart
5	chr12:46868200-46879200	Weak transcription	Primary B cells from peripheral blood	blood
6	chr12:46868600-46883000	Weak transcription	Left Ventricle	heart
7	chr12:46868600-46883400	Weak transcription	Psoas Muscle	Psoas
8	chr12:46868600-46889200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:46868800-46883400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr12:46868800-46886000	Weak transcription	HSMMtube	muscle
11	chr12:46870400-46880400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr12:46871200-46887800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr12:46873000-46880400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr12:46873600-46886000	Weak transcription	HSMM	muscle
15	chr12:46874000-46880400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr12:46874800-46883400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr12:46875600-46878800	Enhancers	Primary hematopoietic stem cells	blood
18	chr12:46875800-46878800	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr12:46876000-46878600	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr12:46876000-46878600	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr12:46876000-46879200	Enhancers	Hela-S3	cervix
22	chr12:46876200-46878600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr12:46876400-46878800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr12:46876400-46879400	Enhancers	K562	blood
25	chr12:46876600-46880400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr12:46877400-46878600	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr12:46877400-46878600	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr12:46877600-46879200	Weak transcription	Primary B cells from cord blood	blood
29	chr12:46877600-46881200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr12:46877800-46883200	Weak transcription	NHEK	skin
31	chr12:46878000-46881000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr12:46878000-46883200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr12:46878000-46883400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr12:46878000-46883400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr12:46878000-46883400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr12:46878000-46885400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr12:46878000-46887400	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr12:46878200-46879200	Weak transcription	A549	lung
39	chr12:46878200-46879400	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr12:46878200-46879400	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr12:46878200-46879600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr12:46878200-46880400	Weak transcription	Placenta	Placenta
43	chr12:46878200-46881400	Weak transcription	Osteobl	bone
44	chr12:46878200-46882400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr12:46878200-46883000	Weak transcription	Ovary	ovary
46	chr12:46878200-46883000	Weak transcription	HMEC	breast
47	chr12:46878200-46883200	Weak transcription	NHLF	lung
48	chr12:46878200-46883400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr12:46878200-46883400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr12:46878200-46883400	Weak transcription	Liver	Liver

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