Variant report

Variant	rs4246261
Chromosome Location	chr12:104571014-104571015
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104530177..104533540-chr12:104569302..104573926,9	MCF-7	breast:
2	chr12:104571005..104572580-chr12:104577210..104579491,2	MCF-7	breast:
3	chr12:104570809..104571731-chr12:104687793..104688584,2	MCF-7	breast:
4	chr12:104564791..104567133-chr12:104568799..104572664,3	K562	blood:
5	chr12:104570742..104573318-chr12:104574956..104577002,2	K562	blood:
6	chr12:104528363..104533397-chr12:104570131..104576145,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000120837	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11111916	0.92[ASN][1000 genomes]
rs11111917	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11111940	0.83[EUR][1000 genomes]
rs11613944	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11829709	0.89[ASN][1000 genomes]
rs11836726	0.88[ASN][1000 genomes]
rs4246260	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4321026	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4371000	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4522249	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4964626	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4964628	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4964678	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61939220	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7297296	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7297956	0.83[EUR][1000 genomes]
rs7957744	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7961381	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7966970	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7969538	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7972172	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7975524	0.80[EUR][1000 genomes]
rs9668556	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9705582	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045725	chr12:104524153-104614108	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	n/a
2	nsv541586	chr12:104524153-104614108	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	n/a
3	esv1842062	chr12:104531180-104638773	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	n/a
4	nsv899493	chr12:104548613-104703228	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv899494	chr12:104561521-104806232	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4246261	EID3	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104566400-104573400	Weak transcription	Spleen	Spleen
2	chr12:104570000-104573000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr12:104570600-104571200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr12:104570800-104572400	Flanking Active TSS	A549	lung
5	chr12:104570800-104572600	Enhancers	NHLF	lung
6	chr12:104570800-104572800	Enhancers	Rectal Smooth Muscle	rectum
7	chr12:104571000-104571200	Enhancers	Muscle Satellite Cultured Cells	--
8	chr12:104571000-104571200	Enhancers	HSMM	muscle
9	chr12:104571000-104571400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr12:104571000-104571400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr12:104571000-104571600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr12:104571000-104571600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr12:104571000-104571600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr12:104571000-104571600	Enhancers	HSMMtube	muscle
15	chr12:104571000-104571600	Enhancers	Osteobl	bone
16	chr12:104571000-104571800	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr12:104571000-104571800	Enhancers	Lung	lung
18	chr12:104571000-104571800	Enhancers	HUVEC	blood vessel
19	chr12:104571000-104572200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr12:104571000-104572200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr12:104571000-104572200	Enhancers	Adipose Nuclei	Adipose
22	chr12:104571000-104572200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr12:104571000-104572200	Enhancers	Fetal Lung	lung
24	chr12:104571000-104572200	Enhancers	K562	blood
25	chr12:104571000-104572400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr12:104571000-104572400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr12:104571000-104572400	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr12:104571000-104572400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr12:104571000-104572400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr12:104571000-104572400	Enhancers	NH-A	brain
31	chr12:104571000-104572400	Enhancers	NHDF-Ad	bronchial
32	chr12:104571000-104572600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr12:104571000-104572600	Enhancers	Placenta	Placenta
34	chr12:104571000-104572600	Flanking Active TSS	Hela-S3	cervix
35	chr12:104571000-104572600	Enhancers	HMEC	breast
36	chr12:104571000-104573000	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr12:104571000-104573200	Enhancers	Colon Smooth Muscle	Colon
38	chr12:104571000-104576600	Enhancers	Breast Myoepithelial Primary Cells	Breast

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