Variant report

Variant	rs12085966
Chromosome Location	chr1:48229395-48229396
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr1:48229230-48229847	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr1:48229358-48229826	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr1:48229161-48229910	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr1:48229311-48229915	MCF10A-Er-Src	breast:	n/a	n/a
5	MYC	chr1:48229052-48229910	MCF10A-Er-Src	breast:	n/a	n/a
6	CTCF	chr1:48229380-48229530	GM12873	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:48221337..48224039-chr1:48227721..48230419,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000273395	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12028640	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12038078	0.88[CHD][hapmap]
rs12040464	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12045022	1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4927044	0.91[CEU][hapmap];0.85[CHB][hapmap];0.81[EUR][1000 genomes];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	nsv829760	chr1:48111126-48308188	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv871257	chr1:48111699-48334490	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv871175	chr1:48150309-48254782	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1001126	chr1:48164622-48320862	Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1003161	chr1:48207715-48286563	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:48215400-48236200	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr1:48218600-48239800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr1:48222400-48231800	Weak transcription	Pancreas	Pancrea
4	chr1:48224400-48230400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:48225400-48231600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:48225400-48234000	Enhancers	Right Atrium	heart
7	chr1:48225600-48230000	Weak transcription	Fetal Intestine Small	intestine
8	chr1:48225600-48237000	Weak transcription	Fetal Intestine Large	intestine
9	chr1:48226600-48231600	Weak transcription	Brain Germinal Matrix	brain
10	chr1:48227000-48233600	Weak transcription	Hela-S3	cervix
11	chr1:48228000-48238800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:48228200-48230400	Enhancers	Esophagus	oesophagus
13	chr1:48228200-48238000	Weak transcription	Spleen	Spleen
14	chr1:48228400-48230400	Enhancers	Fetal Muscle Leg	muscle
15	chr1:48228600-48229600	Enhancers	Stomach Smooth Muscle	stomach
16	chr1:48228600-48230400	Enhancers	Aorta	Aorta
17	chr1:48228800-48230000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:48228800-48230400	Enhancers	HMEC	breast
19	chr1:48228800-48231200	Enhancers	Placenta	Placenta
20	chr1:48229000-48229600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
21	chr1:48229000-48230000	Enhancers	Fetal Muscle Trunk	muscle
22	chr1:48229000-48230200	Enhancers	NHEK	skin
23	chr1:48229000-48230400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:48229000-48230400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:48229000-48230800	Enhancers	Fetal Heart	heart
26	chr1:48229000-48231000	Enhancers	Lung	lung
27	chr1:48229200-48229600	Enhancers	Fetal Lung	lung
28	chr1:48229200-48229800	Enhancers	Left Ventricle	heart
29	chr1:48229200-48230000	Bivalent Enhancer	Fetal Stomach	stomach
30	chr1:48229200-48231600	Enhancers	Right Ventricle	heart

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