Variant report

Variant	rs1949424
Chromosome Location	chr2:99468341-99468342
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	chr2:99466677..99468952-chr2:99480016..99482903,2	MCF-7	breast:
2	chr2:99468266..99471087-chr2:99473957..99476591,2	MCF-7	breast:

Extended variants
information (count: 65 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10169003	0.88[ASN][1000 genomes]
rs10175560	0.87[EUR][1000 genomes]
rs10181972	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10192266	0.85[EUR][1000 genomes]
rs11123756	0.91[EUR][1000 genomes]
rs11887536	0.84[ASN][1000 genomes]
rs11900176	0.88[CEU][hapmap];0.82[CHD][hapmap];0.80[MKK][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs11900524	0.87[EUR][1000 genomes]
rs12474283	0.80[CEU][hapmap]
rs12478574	0.92[EUR][1000 genomes]
rs12712033	0.87[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12712034	0.87[CEU][hapmap];0.89[EUR][1000 genomes]
rs12712037	0.88[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs12712040	0.89[EUR][1000 genomes]
rs12712042	0.84[EUR][1000 genomes]
rs12990579	0.88[CEU][hapmap];0.83[CHB][hapmap];0.87[EUR][1000 genomes]
rs12992214	0.88[ASN][1000 genomes]
rs13004700	0.80[CEU][hapmap]
rs13004923	0.89[ASN][1000 genomes]
rs13005124	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs13005148	0.92[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs13024838	0.84[EUR][1000 genomes]
rs13028500	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs1581249	0.89[EUR][1000 genomes]
rs1581250	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17758170	0.92[CEU][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs1878585	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1878589	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs1962029	0.91[EUR][1000 genomes]
rs1983352	0.87[GIH][hapmap];0.83[MEX][hapmap]
rs2048949	0.80[EUR][1000 genomes]
rs2280256	0.83[MEX][hapmap]
rs4311103	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs4499468	0.92[EUR][1000 genomes]
rs4553869	0.91[EUR][1000 genomes]
rs4850890	0.84[EUR][1000 genomes]
rs4851174	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs4851175	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs4851176	0.84[EUR][1000 genomes]
rs6542841	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs6542845	0.84[EUR][1000 genomes]
rs6704682	0.91[EUR][1000 genomes]
rs6724477	0.92[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs6726156	0.92[ASN][1000 genomes]
rs6739097	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6741166	0.84[EUR][1000 genomes]
rs6742047	0.84[EUR][1000 genomes]
rs6752025	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6757098	0.96[CEU][hapmap];0.82[CHD][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs6760065	0.96[CEU][hapmap];0.82[CHD][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs7423519	0.92[CEU][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs7565510	0.91[EUR][1000 genomes]
rs7565614	0.87[EUR][1000 genomes]
rs7565736	0.86[EUR][1000 genomes]
rs7565819	0.84[EUR][1000 genomes]
rs7588441	0.84[EUR][1000 genomes]
rs7590596	0.94[EUR][1000 genomes]
rs7593332	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7608889	0.81[CEU][hapmap]
rs883773	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs925887	0.83[CEU][hapmap];0.84[GIH][hapmap]
rs981602	0.82[GIH][hapmap];0.83[MEX][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	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1949424	UNC50	cis	cerebellum	SCAN
rs1949424	TSGA10	cis	cerebellum	SCAN
rs1949424	TSGA10	cis	multi-tissue	Pritchard
rs1949424	LIPT1	cis	cerebellum	SCAN
rs1949424	LIPT1	cis	parietal	SCAN

Chromatin state (count:5 , 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	chr2:99463400-99485400	Weak transcription	Gastric	stomach
5	chr2:99466000-99468800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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