Variant report

Variant	rs12463612
Chromosome Location	chr2:173922213-173922214
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:173920583..173924312-chr2:173940394..173943115,4	MCF-7	breast:
2	chr2:173914253..173918906-chr2:173919243..173923517,5	MCF-7	breast:
3	chr2:173922130..173925125-chr2:173934034..173936913,2	K562	blood:

Variant related genes	Relation type
ENSG00000091436	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10497403	0.88[GIH][hapmap]
rs11680555	0.80[CEU][hapmap]
rs11687520	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11687539	0.87[CEU][hapmap]
rs12464956	0.88[GIH][hapmap]
rs1551249	0.83[CEU][hapmap];0.84[GIH][hapmap]
rs17710065	0.80[CEU][hapmap]
rs17710437	0.86[CEU][hapmap]
rs1809139	0.80[CEU][hapmap]
rs1973037	0.83[CEU][hapmap];0.84[GIH][hapmap]
rs3754747	0.87[CEU][hapmap];0.85[TSI][hapmap]
rs3754749	0.94[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3769213	0.83[CEU][hapmap];0.83[GIH][hapmap]
rs3820835	0.88[CEU][hapmap]
rs4972529	0.88[CEU][hapmap]
rs61151985	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62175799	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6433392	0.85[ASW][hapmap];0.85[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6717529	0.83[CEU][hapmap];0.85[GIH][hapmap]
rs6717735	0.83[CEU][hapmap];0.83[GIH][hapmap]
rs6742219	0.86[CEU][hapmap]
rs734993	0.86[CEU][hapmap];0.84[TSI][hapmap]
rs746179	0.87[CEU][hapmap]
rs7599340	0.81[CEU][hapmap]
rs935006	0.80[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834459	chr2:173735192-173926750	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1011724	chr2:173916482-174231908	Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv834460	chr2:173919464-174085288	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12463612	CYBRD1	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173908800-173924200	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr2:173914800-173923400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr2:173914800-173923400	Weak transcription	Liver	Liver
4	chr2:173915200-173924000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:173915200-173929200	Weak transcription	Fetal Lung	lung
6	chr2:173916800-173923600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:173916800-173927600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:173918400-173923000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr2:173920600-173923000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr2:173920600-173924200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr2:173920600-173937200	Weak transcription	Psoas Muscle	Psoas
12	chr2:173920800-173922800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:173921200-173925600	Enhancers	Adipose Nuclei	Adipose
14	chr2:173921200-173926400	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr2:173921400-173922600	Enhancers	NHDF-Ad	bronchial
16	chr2:173921400-173923400	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr2:173921400-173923400	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr2:173921400-173923600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr2:173921600-173923600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr2:173921600-173923800	Weak transcription	NHEK	skin
21	chr2:173921800-173923000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr2:173921800-173923200	Weak transcription	Right Atrium	heart
23	chr2:173921800-173923400	Weak transcription	Lung	lung
24	chr2:173921800-173923400	Weak transcription	Spleen	Spleen
25	chr2:173922000-173924800	Weak transcription	Ovary	ovary
26	chr2:173922000-173926000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr2:173922200-173923800	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr2:173922200-173924400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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