Variant report

Variant	rs11900176
Chromosome Location	chr2:99463536-99463537
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	chr2:99461401..99464766-chr2:99483724..99486615,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196872	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10175560	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10182043	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10202643	0.82[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11123754	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11123756	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11900524	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12478574	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12712033	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs12712034	0.91[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12712037	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12712039	0.83[ASN][1000 genomes]
rs12712040	0.86[EUR][1000 genomes]
rs12990579	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13005148	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13024838	0.82[EUR][1000 genomes]
rs1517682	0.89[ASW][hapmap];0.81[LWK][hapmap];0.81[MKK][hapmap];0.84[AFR][1000 genomes]
rs1581249	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17758170	0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs1878589	0.83[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes]
rs1949424	0.87[EUR][1000 genomes]
rs1962029	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2280142	0.82[CEU][hapmap];0.89[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4499468	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4553869	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6542837	0.83[ASW][hapmap];0.82[CEU][hapmap];0.81[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6542839	0.86[MEX][hapmap];0.83[MKK][hapmap]
rs6542841	0.84[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6704682	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6714330	0.89[AMR][1000 genomes]
rs6724477	0.81[TSI][hapmap]
rs6739097	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs6741166	0.82[EUR][1000 genomes]
rs6752025	0.83[EUR][1000 genomes]
rs6753465	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6753879	0.91[AMR][1000 genomes]
rs6755640	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6757098	0.84[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6760065	0.84[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.90[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7423519	0.83[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs7560696	0.82[CEU][hapmap];0.84[AMR][1000 genomes]
rs7565510	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7565614	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7565736	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7565819	0.82[EUR][1000 genomes]
rs7588441	0.82[EUR][1000 genomes]
rs7590596	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7593332	0.87[EUR][1000 genomes]
rs883773	0.84[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs885115	0.95[AMR][1000 genomes];0.91[EUR][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	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv582517	chr2:99440917-99487972	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11900176	TSGA10	cis	cerebellum	SCAN
rs11900176	FER1L5	cis	cerebellum	SCAN
rs11900176	TSGA10	cis	multi-tissue	Pritchard

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99450000-99468400	Weak transcription	Fetal Intestine Small	intestine
2	chr2:99453200-99473200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr2:99456200-99473000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:99461600-99464800	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr2:99462400-99464800	Enhancers	NHDF-Ad	bronchial
6	chr2:99462400-99465000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:99463400-99463800	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr2:99463400-99465600	Weak transcription	Pancreas	Pancrea
9	chr2:99463400-99485400	Weak transcription	Gastric	stomach

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