Variant report

Variant	rs575657
Chromosome Location	chr12:63266130-63266131
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:63263678..63269164-chr12:63325830..63330278,6	MCF-7	breast:
2	chr12:63260158..63264907-chr12:63265796..63270388,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000252660	Chromatin interaction
ENSG00000111110	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11174704	0.92[CEU][hapmap]
rs2594711	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2839798	0.97[CHD][hapmap]
rs479356	0.92[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs481867	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs482794	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs540694	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs572873	0.92[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs599969	0.89[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs629499	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs688624	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs699567	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs699568	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs771973	0.86[CEU][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3415227	chr12:63228121-63591615	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs575657	C12orf61	cis	parietal	SCAN
rs575657	MON2	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:63258200-63277200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr12:63260200-63275400	Weak transcription	Pancreas	Pancrea
3	chr12:63260600-63270600	Weak transcription	Aorta	Aorta
4	chr12:63260800-63267000	Weak transcription	Placenta	Placenta
5	chr12:63260800-63270000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr12:63260800-63275200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr12:63261200-63275000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr12:63261200-63277800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr12:63261400-63266800	Weak transcription	Fetal Intestine Small	intestine
10	chr12:63261800-63267000	Weak transcription	Fetal Intestine Large	intestine
11	chr12:63262000-63269600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr12:63262200-63266800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr12:63262200-63267200	Weak transcription	K562	blood
14	chr12:63262400-63269600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr12:63262400-63275200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr12:63262400-63277000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:63262600-63267200	Weak transcription	A549	lung
18	chr12:63262600-63267800	Weak transcription	Brain Angular Gyrus	brain
19	chr12:63262600-63267800	Weak transcription	Brain Substantia Nigra	brain
20	chr12:63262800-63276000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr12:63263400-63267000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr12:63263400-63277200	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr12:63264000-63270200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr12:63264400-63268400	Weak transcription	HepG2	liver
25	chr12:63265800-63266200	Enhancers	Brain Hippocampus Middle	brain

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