Variant report

Variant	rs1492480
Chromosome Location	chr3:111860222-111860223
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	chr3:111859837..111862167-chr3:112256624..112258984,2	MCF-7	breast:
2	chr3:111858864..111861858-chr3:112359276..112360974,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144848	Chromatin interaction
ENSG00000091986	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10511306	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10511307	0.84[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11928130	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13059342	0.81[CHB][hapmap]
rs13069933	0.94[ASN][1000 genomes]
rs13078713	0.90[CHB][hapmap]
rs1388855	0.84[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1492481	0.94[ASN][1000 genomes]
rs1492483	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.92[MEX][hapmap];0.80[MKK][hapmap];0.86[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1492484	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1492485	0.95[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs1492486	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs1602672	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1948404	0.84[CEU][hapmap]
rs1994772	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2029638	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35411358	0.82[EUR][1000 genomes]
rs7651558	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs879652	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs950528	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010219	chr3:111856709-111923647	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1492480	CD200	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111852200-111863400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:111853400-111867400	Weak transcription	Gastric	stomach
3	chr3:111856200-111867400	Weak transcription	Thymus	Thymus
4	chr3:111856200-111867600	Weak transcription	Left Ventricle	heart
5	chr3:111856400-111861800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr3:111856400-111862400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr3:111857000-111861000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr3:111858800-111862400	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr3:111860200-111860400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:111860200-111860600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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