Variant report

Variant	rs12464956
Chromosome Location	chr2:173917659-173917660
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:173914253..173918906-chr2:173919243..173923517,5	MCF-7	breast:
2	chr2:173907933..173910689-chr2:173917476..173919133,2	K562	blood:
3	chr2:173907898..173920360-chr2:173936226..173946823,30	MCF-7	breast:
4	chr2:173902789..173904327-chr2:173917257..173919132,2	K562	blood:
5	chr2:173914464..173920190-chr2:173936598..173942304,10	MCF-7	breast:
6	chr2:173915281..173918065-chr2:173919671..173921677,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091436	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1020599	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10497403	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.94[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12463612	0.88[GIH][hapmap]
rs12474338	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12474484	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1551249	0.87[ASW][hapmap];0.94[CEU][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap];0.94[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1973037	0.88[ASW][hapmap];0.94[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap];0.94[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2012213	0.82[ASW][hapmap];0.83[TSI][hapmap]
rs3769210	0.81[CHB][hapmap];0.86[CHD][hapmap];0.80[GIH][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs3769211	0.84[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs3769213	0.88[ASW][hapmap];0.94[CEU][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60121307	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6433392	0.84[GIH][hapmap]
rs6717489	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6717529	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6717735	0.82[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6742219	0.93[CEU][hapmap];0.81[CHB][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12464956	CYBRD1	cis	parietal	SCAN
rs12464956	ZAK	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173893200-173922000	Weak transcription	Brain Anterior Caudate	brain
2	chr2:173901000-173918000	Weak transcription	Brain Angular Gyrus	brain
3	chr2:173904400-173921400	Weak transcription	Ovary	ovary
4	chr2:173908600-173921400	Weak transcription	Left Ventricle	heart
5	chr2:173908800-173924200	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr2:173911800-173918200	Weak transcription	Fetal Heart	heart
7	chr2:173914400-173917800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr2:173914800-173918200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr2:173914800-173921600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr2:173914800-173923400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr2:173914800-173923400	Weak transcription	Liver	Liver
12	chr2:173915000-173921400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr2:173915200-173918000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr2:173915200-173918400	Weak transcription	Adipose Nuclei	Adipose
15	chr2:173915200-173918400	Weak transcription	Osteobl	bone
16	chr2:173915200-173924000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr2:173915200-173929200	Weak transcription	Fetal Lung	lung
18	chr2:173915400-173917800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:173915400-173917800	Weak transcription	NHDF-Ad	bronchial
20	chr2:173915400-173918000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr2:173915400-173918400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:173915800-173917800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:173915800-173917800	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr2:173915800-173920400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr2:173915800-173921400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr2:173916000-173917800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr2:173916600-173917800	Weak transcription	A549	lung
28	chr2:173916800-173918000	Weak transcription	NHEK	skin
29	chr2:173916800-173918400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr2:173916800-173923600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr2:173916800-173927600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr2:173917000-173920200	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr2:173917200-173921400	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr2:173917600-173917800	Enhancers	Colon Smooth Muscle	Colon
35	chr2:173917600-173918000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr2:173917600-173918600	Enhancers	Hela-S3	cervix
37	chr2:173917600-173918600	Enhancers	HSMM	muscle
38	chr2:173917600-173919800	Enhancers	HepG2	liver

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