Variant report

Variant	rs7871537
Chromosome Location	chr9:95553948-95553949
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:95478444..95479282-chr9:95553871..95554503,2	MCF-7	breast:
2	chr9:95548519..95551423-chr9:95551697..95555504,3	K562	blood:
3	chr9:95548536..95551423-chr9:95551697..95554622,2	K562	blood:
4	chr9:95262989..95265065-chr9:95551736..95554056,2	MCF-7	breast:
5	chr9:95490525..95493250-chr9:95553271..95556888,4	MCF-7	breast:
6	chr9:95431446..95434360-chr9:95553227..95554835,2	K562	blood:
7	chr9:95477589..95479745-chr9:95552939..95554698,2	K562	blood:

Variant related genes	Relation type
ENSG00000127080	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1010823	0.82[AMR][1000 genomes]
rs10117377	0.98[ASN][1000 genomes]
rs10820997	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs10821009	0.93[CEU][hapmap];0.95[JPT][hapmap]
rs10821010	0.94[CEU][hapmap];0.95[JPT][hapmap]
rs10821012	0.93[CEU][hapmap];0.95[JPT][hapmap]
rs10821016	0.82[AMR][1000 genomes]
rs10992407	0.80[CEU][hapmap]
rs10992413	0.94[CEU][hapmap];0.95[JPT][hapmap]
rs10992414	0.80[CEU][hapmap];0.83[JPT][hapmap]
rs10992418	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10992430	0.94[CEU][hapmap];0.95[JPT][hapmap]
rs10992431	0.94[CEU][hapmap];0.95[JPT][hapmap]
rs10992432	0.94[CEU][hapmap];0.95[JPT][hapmap]
rs10992434	0.93[CEU][hapmap];0.95[JPT][hapmap]
rs10992436	0.95[JPT][hapmap];0.81[YRI][hapmap]
rs10992442	0.93[CEU][hapmap];0.95[JPT][hapmap]
rs10992443	0.94[CEU][hapmap];0.95[JPT][hapmap]
rs10992444	0.93[CEU][hapmap];0.95[JPT][hapmap]
rs10992445	0.93[CEU][hapmap];0.95[JPT][hapmap]
rs10992447	0.84[CEU][hapmap]
rs10992448	0.84[CEU][hapmap];0.86[JPT][hapmap]
rs10992451	0.94[CEU][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes]
rs10992453	0.80[CEU][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes]
rs10992456	0.82[AMR][1000 genomes]
rs10992460	0.84[CEU][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10992461	0.84[CEU][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10992462	0.84[AMR][1000 genomes]
rs10992469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[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	0.94[CEU][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes]
rs1125064	0.94[CEU][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes]
rs11535540	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12236393	0.94[CEU][hapmap];0.95[JPT][hapmap]
rs12236516	0.94[CEU][hapmap];0.95[JPT][hapmap]
rs12236754	0.86[JPT][hapmap]
rs12238691	0.80[CEU][hapmap];0.87[JPT][hapmap]
rs12684587	0.82[AMR][1000 genomes]
rs12685080	1.00[CEU][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12685257	0.93[CEU][hapmap];0.95[JPT][hapmap]
rs12685780	0.93[CEU][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes]
rs12685791	1.00[CEU][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes]
rs12686771	0.84[CEU][hapmap]
rs1555574	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16908555	0.84[CEU][hapmap]
rs1810696	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1853428	0.84[CEU][hapmap]
rs1974004	0.84[CEU][hapmap]
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]
rs2181584	0.80[CEU][hapmap];0.87[JPT][hapmap]
rs2181586	0.94[CEU][hapmap];0.95[JPT][hapmap]
rs2274413	0.80[CEU][hapmap]
rs2296080	0.93[CEU][hapmap];0.95[JPT][hapmap]
rs3203916	0.93[CEU][hapmap];0.95[JPT][hapmap]
rs3739605	0.84[CEU][hapmap];0.86[JPT][hapmap]
rs4545157	0.83[AMR][1000 genomes]
rs556	0.93[CEU][hapmap];0.95[JPT][hapmap]
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	0.84[CEU][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes]
rs753802	0.95[JPT][hapmap]
rs753803	0.94[CEU][hapmap];0.95[JPT][hapmap]
rs7850075	0.84[CEU][hapmap]
rs7860628	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7862106	1.00[CEU][hapmap];0.95[JPT][hapmap];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]
rs7875225	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs8181065	0.94[CEU][hapmap];0.95[JPT][hapmap]
rs878610	0.82[AMR][1000 genomes]
rs976320	0.83[CHB][hapmap];0.94[JPT][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	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
rs7871537	BICD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 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	chr9:95553200-95556600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr9:95553600-95557400	Weak transcription	Liver	Liver
4	chr9:95553800-95554000	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr9:95553800-95554000	Bivalent Enhancer	GM12878-XiMat	blood

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