Variant report

Variant	rs2249933
Chromosome Location	chr1:160949114-160949115
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:160948860..160950429-chr1:160950620..160952705,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10737178	0.83[CHB][hapmap];0.87[CHD][hapmap]
rs10908820	0.80[ASN][1000 genomes]
rs12132502	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2039223	0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2184065	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2245672	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2246145	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2246484	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2246485	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2247472	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2249409	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2250174	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2250193	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2250304	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2256505	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2256625	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2265239	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2265240	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2265242	0.86[AMR][1000 genomes]
rs2481073	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2481076	0.84[ASN][1000 genomes]
rs2481077	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2483139	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2483140	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2483141	0.92[CEU][hapmap];0.92[CHB][hapmap];0.87[YRI][hapmap]
rs2483142	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2779801	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2988722	0.80[AMR][1000 genomes]
rs2990694	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2990706	0.81[EUR][1000 genomes]
rs3007155	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4483427	0.96[ASN][1000 genomes]
rs6427563	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6427571	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6677526	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6677533	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7542911	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs790055	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs790056	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv548058	chr1:160925455-160989614	Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2249933	ITLN2	cis	Whole Blood	GTEx
rs2249933	TSTD1	cis	Nerve Tibial	GTEx
rs2249933	NHLH1	cis	parietal	SCAN
rs2249933	F11R	Cis_1M	lymphoblastoid	RTeQTL
rs2249933	F11R	cis	cerebellum	SCAN
rs2249933	USF1	cis	multi-tissue	Pritchard
rs2249933	F11R	cis	parietal	SCAN
rs2249933	PAQR6	cis	cerebellum	SCAN
rs2249933	F11R	cis	lymphoblastoid	seeQTL
rs2249933	OR6K3	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160943200-160951000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:160943200-160959800	Weak transcription	Pancreas	Pancrea
3	chr1:160943600-160949200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr1:160943800-160950600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:160944000-160950600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr1:160947000-160950600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr1:160948600-160968000	Weak transcription	Ovary	ovary

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