Variant report

Variant	rs564501
Chromosome Location	chr12:63201265-63201266
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:62994530..62996807-chr12:63199626..63201267,3	MCF-7	breast:
2	chr12:63199599..63203021-chr12:63327294..63329908,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000252660	Chromatin interaction
ENSG00000111110	Chromatin interaction
ENSG00000257354	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs2652029	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2652030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2663955	0.81[AFR][1000 genomes]
rs2663957	0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2704761	0.81[AFR][1000 genomes]
rs2704764	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs337516	0.85[YRI][hapmap]
rs337517	0.85[YRI][hapmap]
rs500505	0.82[YRI][hapmap]
rs518285	0.88[YRI][hapmap]
rs535206	0.81[LWK][hapmap];0.85[MKK][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs536052	0.81[AFR][1000 genomes]
rs563718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs639821	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs679811	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv899160	chr12:63149213-63209623	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs564501	AGAP2	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:63175200-63206800	Weak transcription	Pancreas	Pancrea
2	chr12:63187800-63205200	Weak transcription	K562	blood
3	chr12:63187800-63206400	Weak transcription	Osteobl	bone
4	chr12:63187800-63206800	Weak transcription	Duodenum Mucosa	Duodenum
5	chr12:63187800-63211400	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr12:63188000-63206800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr12:63192800-63211400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr12:63193000-63201400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr12:63193400-63206800	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr12:63195400-63206000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr12:63195600-63211400	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr12:63195600-63211400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr12:63195800-63228600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr12:63196000-63206600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr12:63196000-63206800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr12:63196000-63206800	Weak transcription	Fetal Intestine Large	intestine
17	chr12:63196000-63206800	Weak transcription	Right Ventricle	heart
18	chr12:63196000-63213600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr12:63196000-63213800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr12:63196000-63225800	Weak transcription	Gastric	stomach
21	chr12:63196400-63201400	Weak transcription	HepG2	liver
22	chr12:63196400-63213600	Weak transcription	Fetal Intestine Small	intestine
23	chr12:63197400-63206600	Weak transcription	Brain Angular Gyrus	brain
24	chr12:63198000-63206000	Weak transcription	Brain Hippocampus Middle	brain
25	chr12:63198000-63206600	Weak transcription	Brain Substantia Nigra	brain
26	chr12:63199200-63206600	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr12:63199400-63201400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr12:63200600-63206800	Weak transcription	Lung	lung
29	chr12:63201000-63201600	Weak transcription	Primary hematopoietic stem cells	blood
30	chr12:63201000-63201800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr12:63201200-63201800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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