Variant report

Variant	rs10497403
Chromosome Location	chr2:173919485-173919486
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:173919027..173921346-chr2:173933987..173935523,2	MCF-7	breast:
2	chr2:173907898..173920360-chr2:173936226..173946823,30	MCF-7	breast:
3	chr2:173914464..173920190-chr2:173936598..173942304,10	MCF-7	breast:
4	chr2:173919334..173920934-chr2:173923868..173926375,2	K562	blood:
5	chr2:173914253..173918906-chr2:173919243..173923517,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091436	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1020599	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12463612	0.88[GIH][hapmap]
rs12464956	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]
rs12474338	0.82[ASN][1000 genomes]
rs12474484	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1551249	0.94[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1973037	0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap];0.89[YRI][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2012213	0.82[CHD][hapmap]
rs3769201	0.84[CHD][hapmap]
rs3769210	0.81[CHB][hapmap];0.82[CHD][hapmap];0.80[GIH][hapmap]
rs3769211	0.84[CEU][hapmap];0.81[CHB][hapmap]
rs3769213	0.94[CEU][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60121307	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6433392	0.84[GIH][hapmap]
rs6717489	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6717529	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6717735	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6742219	0.93[CEU][hapmap];0.81[CHB][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10497403	CYBRD1	cis	parietal	SCAN
rs10497403	ZAK	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173893200-173922000	Weak transcription	Brain Anterior Caudate	brain
2	chr2:173904400-173921400	Weak transcription	Ovary	ovary
3	chr2:173908600-173921400	Weak transcription	Left Ventricle	heart
4	chr2:173908800-173924200	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr2:173914800-173921600	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr2:173914800-173923400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr2:173914800-173923400	Weak transcription	Liver	Liver
8	chr2:173915000-173921400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr2:173915200-173924000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:173915200-173929200	Weak transcription	Fetal Lung	lung
11	chr2:173915800-173920400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:173915800-173921400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:173916800-173923600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:173916800-173927600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr2:173917000-173920200	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr2:173917200-173921400	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr2:173917600-173919800	Enhancers	HepG2	liver
18	chr2:173917800-173919800	Enhancers	A549	lung
19	chr2:173918000-173919800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr2:173918200-173921400	Weak transcription	NHDF-Ad	bronchial
21	chr2:173918400-173919800	Enhancers	Osteobl	bone
22	chr2:173918400-173920600	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr2:173918400-173923000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr2:173918800-173922000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:173919000-173920400	Weak transcription	Adipose Nuclei	Adipose
26	chr2:173919000-173921800	Weak transcription	Placenta	Placenta
27	chr2:173919200-173921600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr2:173919400-173920200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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