Variant report

Variant	rs1555574
Chromosome Location	chr9:95551951-95551952
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:95548519..95551423-chr9:95551697..95555504,3	K562	blood:
2	chr9:95548536..95551423-chr9:95551697..95554622,2	K562	blood:
3	chr9:95262989..95265065-chr9:95551736..95554056,2	MCF-7	breast:
4	chr9:95488503..95490523-chr9:95550611..95553154,2	MCF-7	breast:
5	chr9:95525165..95529310-chr9:95549740..95553522,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185963	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1010823	0.82[AMR][1000 genomes]
rs10117377	0.98[ASN][1000 genomes]
rs10820997	0.83[EUR][1000 genomes]
rs10821014	0.82[AFR][1000 genomes]
rs10821016	0.82[AMR][1000 genomes]
rs10992418	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10992451	0.82[AMR][1000 genomes]
rs10992453	0.82[AMR][1000 genomes]
rs10992456	0.82[AMR][1000 genomes]
rs10992460	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10992461	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10992462	0.84[AMR][1000 genomes]
rs10992469	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992472	0.89[ASN][1000 genomes]
rs1125063	0.82[AMR][1000 genomes]
rs1125064	0.82[AMR][1000 genomes]
rs11535540	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12684587	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12685080	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12685780	0.82[AMR][1000 genomes]
rs12685791	0.82[AMR][1000 genomes]
rs1810696	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2146719	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2181521	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4545157	0.83[AMR][1000 genomes]
rs56111209	0.84[AMR][1000 genomes]
rs56311406	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57737182	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs60457563	0.84[AMR][1000 genomes]
rs68022962	0.84[AMR][1000 genomes]
rs7031163	0.82[AMR][1000 genomes]
rs7860628	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7862106	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7863741	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7868651	0.94[ASN][1000 genomes]
rs7871537	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7875225	0.98[ASN][1000 genomes]
rs878610	0.82[AMR][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	nsv430081	chr9:95502571-95568110	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv831654	chr9:95542920-95720961	ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv982595	chr9:95551536-95561640	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1555574	BICD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95541400-95558600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:95546000-95553000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr9:95546000-95553000	Weak transcription	NHEK	skin
4	chr9:95551800-95552000	Enhancers	HepG2	liver

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