Variant report

Variant	rs12082238
Chromosome Location	chr1:62760625-62760626
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:62759279..62761889-chr1:62763662..62766108,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000201153	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10493320	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11207957	1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs12058486	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12063531	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12065844	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12078087	1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12079207	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12085325	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12718429	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12724349	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12760226	1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12760895	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2296518	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2477872	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2666487	0.98[ASN][1000 genomes]
rs2666488	0.98[ASN][1000 genomes]
rs2765258	1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs2765261	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2765263	0.81[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34752481	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7520614	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs765691	0.87[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs765692	0.93[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs912894	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs912895	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs912896	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[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	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1009398	chr1:62656660-62780644	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1013582	chr1:62723703-62910632	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases
5	nsv431712	chr1:62759369-62766001	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12082238	DAB1	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62753200-62761600	Weak transcription	Pancreas	Pancrea
2	chr1:62753200-62761600	Weak transcription	Right Atrium	heart
3	chr1:62754400-62773400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:62754800-62765200	Weak transcription	Fetal Heart	heart
5	chr1:62755600-62761000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr1:62756200-62765000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:62756400-62764800	Weak transcription	HepG2	liver
8	chr1:62759800-62761800	Enhancers	Fetal Muscle Trunk	muscle
9	chr1:62759800-62765400	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr1:62759800-62770800	Enhancers	Fetal Muscle Leg	muscle
11	chr1:62760000-62760800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:62760000-62760800	Bivalent Enhancer	Brain Cingulate Gyrus	brain
13	chr1:62760000-62761200	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr1:62760000-62761200	Weak transcription	HSMMtube	muscle
15	chr1:62760000-62761600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:62760000-62762400	Enhancers	H1 Cell Line	embryonic stem cell
17	chr1:62760200-62761000	Weak transcription	Fetal Stomach	stomach
18	chr1:62760200-62761200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:62760200-62761200	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr1:62760200-62761200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr1:62760200-62761600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr1:62760200-62761600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr1:62760400-62760800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr1:62760400-62760800	Weak transcription	HMEC	breast
25	chr1:62760400-62761200	Weak transcription	Brain Hippocampus Middle	brain
26	chr1:62760400-62761200	Weak transcription	Placenta	Placenta
27	chr1:62760400-62762000	Enhancers	Brain Angular Gyrus	brain
28	chr1:62760400-62762400	Enhancers	Primary T cells from cord blood	blood
29	chr1:62760400-62762400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr1:62760600-62761000	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr1:62760600-62761000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:62760600-62761000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:62760600-62761400	Weak transcription	Fetal Thymus	thymus
34	chr1:62760600-62761600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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