Variant report

Variant	rs2649705
Chromosome Location	chr12:106645647-106645648
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	POLR2A	chr12:106645167-106645738	MCF10A-Er-Src	breast:	n/a	n/a
2	CTCF	chr12:106645520-106645670	AG04450	lung:	n/a	n/a
3	CTCF	chr12:106645500-106645650	NHDF-neo	bronchial:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:106634944..106646449-chr12:106667585..106679535,27	MCF-7	breast:
2	chr12:106644967..106648309-chr12:106659700..106662827,5	MCF-7	breast:
3	chr12:106645468..106647361-chr12:106648038..106649886,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258355	TF binding region
CKAP4	TF binding region
ENSG00000238609	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10507209	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap]
rs1148413	0.91[ASW][hapmap];0.88[CEU][hapmap];0.86[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes]
rs1148415	0.88[CEU][hapmap];0.83[CHB][hapmap];0.88[AMR][1000 genomes]
rs1148417	0.84[CEU][hapmap];0.86[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1148419	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1148421	1.00[CEU][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1148422	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1215740	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.85[LWK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1215741	0.81[ASN][1000 genomes]
rs1215753	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1215757	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1215759	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1215761	0.91[ASW][hapmap];0.88[CEU][hapmap];0.86[GIH][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1215807	0.96[CEU][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12227822	0.87[ASN][1000 genomes]
rs12231439	0.87[ASN][1000 genomes]
rs12320181	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1237262	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1238021	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2649718	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2704895	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2704896	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2704898	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2936701	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3741882	0.88[ASN][1000 genomes]
rs61942136	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1799917	chr12:106637876-106649988	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv1834434	chr12:106637876-106649988	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2649705	CCDC53	cis	cerebellum	SCAN
rs2649705	PRDM4	cis	cerebellum	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106642800-106647600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:106642800-106647800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:106642800-106648400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:106643000-106646400	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr12:106643000-106647800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr12:106643200-106645800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr12:106643200-106645800	Enhancers	Primary B cells from peripheral blood	blood
8	chr12:106643200-106646600	Weak transcription	NHEK	skin
9	chr12:106643200-106647200	Weak transcription	Aorta	Aorta
10	chr12:106643200-106647800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:106643200-106647800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:106643200-106647800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr12:106643200-106648800	Weak transcription	Right Atrium	heart
14	chr12:106643400-106648400	Weak transcription	Fetal Lung	lung
15	chr12:106643400-106648400	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr12:106644000-106645800	Weak transcription	Left Ventricle	heart
17	chr12:106644000-106648200	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr12:106644200-106646000	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr12:106644200-106649800	Weak transcription	Fetal Heart	heart
20	chr12:106644400-106649400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr12:106644800-106645800	Enhancers	Fetal Muscle Leg	muscle
22	chr12:106644800-106646000	Enhancers	HSMMtube	muscle
23	chr12:106645000-106645800	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr12:106645000-106645800	Enhancers	Osteobl	bone
25	chr12:106645000-106646000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr12:106645000-106646000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr12:106645000-106646000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr12:106645000-106646000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr12:106645200-106645800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr12:106645200-106645800	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr12:106645200-106645800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr12:106645200-106645800	Flanking Active TSS	Fetal Kidney	kidney
33	chr12:106645200-106646000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr12:106645200-106646000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr12:106645400-106645800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:106645400-106645800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr12:106645400-106645800	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr12:106645400-106645800	Enhancers	HepG2	liver
39	chr12:106645400-106646000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr12:106645400-106646000	Enhancers	HSMM	muscle
41	chr12:106645400-106646200	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr12:106645400-106646200	Enhancers	Placenta	Placenta
43	chr12:106645400-106646200	Enhancers	Spleen	Spleen
44	chr12:106645600-106645800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr12:106645600-106646000	Enhancers	NHLF	lung
46	chr12:106645600-106646200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr12:106645600-106646200	Enhancers	Monocytes-CD14+_RO01746	blood
48	chr12:106645600-106646200	Enhancers	NHDF-Ad	bronchial
49	chr12:106645600-106647800	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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