Variant report

Variant	rs1252289
Chromosome Location	chr12:67412403-67412404
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:67405871..67408664-chr12:67412311..67414518,2	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1109345	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1252290	0.98[EUR][1000 genomes]
rs1252294	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1252295	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs774388	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs774389	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs774390	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs774397	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774398	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs905693	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1036984	chr12:67273098-67427543	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv541524	chr12:67311057-67700349	Strong transcription Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1041160	chr12:67357870-67439696	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv469462	chr12:67361657-67475906	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv559211	chr12:67361657-67475906	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv559212	chr12:67373549-67850925	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv1053249	chr12:67395538-67417828	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv1046591	chr12:67396219-67423067	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv2762986	chr12:67409191-67413365	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:67397000-67412800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:67409800-67412800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:67409800-67420800	Weak transcription	Colon Smooth Muscle	Colon
4	chr12:67409800-67420800	Weak transcription	Right Atrium	heart
5	chr12:67410200-67412600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr12:67410200-67412600	Weak transcription	Fetal Brain Male	brain
7	chr12:67410800-67412600	Weak transcription	Brain Germinal Matrix	brain
8	chr12:67411400-67412800	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr12:67411600-67413200	Enhancers	H9 Cell Line	embryonic stem cell
10	chr12:67411600-67413400	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr12:67411800-67413200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr12:67411800-67413200	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr12:67411800-67413400	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr12:67411800-67413400	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr12:67412000-67412800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr12:67412200-67413000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
17	chr12:67412200-67413200	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr12:67412200-67413200	Enhancers	H1 Cell Line	embryonic stem cell
19	chr12:67412200-67413200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr12:67412200-67413200	Enhancers	NH-A	brain
21	chr12:67412200-67413400	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr12:67412200-67420800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr12:67412400-67412800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr12:67412400-67412800	Enhancers	Fetal Brain Female	brain
25	chr12:67412400-67412800	Enhancers	HMEC	breast
26	chr12:67412400-67413200	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr12:67412400-67413400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:67412400-67413400	Enhancers	Rectal Smooth Muscle	rectum
29	chr12:67412400-67413600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr12:67412400-67414000	Enhancers	Duodenum Smooth Muscle	Duodenum

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