Variant report

Variant	rs12301825
Chromosome Location	chr12:46877663-46877664
allele	A/G
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	chr12:46764328..46767954-chr12:46874214..46878193,4	K562	blood:
3	chr12:46865500..46867657-chr12:46876148..46878526,2	MCF-7	breast:
4	chr12:46762092..46763776-chr12:46876026..46877970,3	K562	blood:
5	chr12:46776527..46778494-chr12:46875801..46877684,2	MCF-7	breast:
6	chr12:46764655..46767393-chr12:46875079..46878516,5	K562	blood:

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

Extended variants
information (count: 34 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10880976	0.87[MEX][hapmap]
rs10880977	0.87[MEX][hapmap]
rs11183519	0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AMR][1000 genomes]
rs12300125	0.87[MEX][hapmap]
rs12311952	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes]
rs12318944	0.95[AMR][1000 genomes]
rs12579010	0.81[AMR][1000 genomes]
rs12579984	0.81[AMR][1000 genomes]
rs12581743	0.81[AMR][1000 genomes]
rs17097079	0.81[AMR][1000 genomes]
rs17097091	0.85[CHB][hapmap];0.81[JPT][hapmap];0.80[YRI][hapmap];0.81[AMR][1000 genomes]
rs1946174	0.91[AMR][1000 genomes]
rs235621	0.81[MEX][hapmap]
rs2408616	0.81[AMR][1000 genomes]
rs2430940	0.87[MEX][hapmap]
rs2471583	0.87[MEX][hapmap]
rs4768124	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4768126	0.81[AMR][1000 genomes]
rs4768740	0.83[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.81[MEX][hapmap];0.81[AMR][1000 genomes]
rs58806862	0.81[AMR][1000 genomes]
rs59408501	0.95[AMR][1000 genomes]
rs7132144	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7136117	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7295471	0.87[MEX][hapmap]
rs7297406	0.93[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7310614	0.83[CHD][hapmap];0.84[JPT][hapmap];0.81[MEX][hapmap]
rs7487359	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7487705	0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7976785	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs977069	0.81[MEX][hapmap]

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:63 , 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	chr12:46875800-46878200	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr12:46875800-46878200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr12:46875800-46878800	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr12:46876000-46878600	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr12:46876000-46878600	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr12:46876000-46879200	Enhancers	Hela-S3	cervix
24	chr12:46876200-46878600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr12:46876400-46878000	Enhancers	HUVEC	blood vessel
26	chr12:46876400-46878200	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr12:46876400-46878200	Enhancers	Muscle Satellite Cultured Cells	--
28	chr12:46876400-46878200	Enhancers	A549	lung
29	chr12:46876400-46878800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:46876400-46879400	Enhancers	K562	blood
31	chr12:46876600-46878000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr12:46876600-46880400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr12:46876800-46878000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr12:46876800-46878200	Enhancers	Osteobl	bone
35	chr12:46877200-46878000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr12:46877200-46878000	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr12:46877200-46878000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr12:46877200-46878200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr12:46877200-46878200	Enhancers	NHDF-Ad	bronchial
40	chr12:46877400-46877800	Enhancers	NHEK	skin
41	chr12:46877400-46878000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr12:46877400-46878200	Enhancers	Liver	Liver
43	chr12:46877400-46878200	Enhancers	Fetal Intestine Small	intestine
44	chr12:46877400-46878200	Flanking Active TSS	HepG2	liver
45	chr12:46877400-46878200	Enhancers	HMEC	breast
46	chr12:46877400-46878200	Enhancers	Monocytes-CD14+_RO01746	blood
47	chr12:46877400-46878400	Enhancers	H1 Cell Line	embryonic stem cell
48	chr12:46877400-46878600	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr12:46877400-46878600	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr12:46877600-46877800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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