Variant report

Variant	rs11042604
Chromosome Location	chr11:10089027-10089028
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:10072496..10075384-chr11:10088083..10089891,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10458929	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10500715	0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs10500717	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10743129	0.81[ASN][1000 genomes]
rs10770079	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10770092	0.83[ASN][1000 genomes]
rs10840330	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10840333	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10840334	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs10840347	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10840348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10840352	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10840359	0.97[ASN][1000 genomes]
rs10840361	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10840362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10840370	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11042558	1.00[CEU][hapmap]
rs11042574	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs11042589	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11042590	0.86[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11042591	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11042592	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11042605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11042606	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11042610	1.00[ASN][1000 genomes]
rs11042613	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11042624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.90[ASN][1000 genomes]
rs11042630	0.82[ASN][1000 genomes]
rs11042634	0.91[ASN][1000 genomes]
rs11042635	0.93[ASN][1000 genomes]
rs11042639	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs11042645	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs11042669	1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap]
rs11530489	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12221716	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12222953	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap]
rs12283105	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12575719	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1372807	0.87[CHB][hapmap];0.88[JPT][hapmap]
rs1442732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[ASN][1000 genomes]
rs16907368	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs16907396	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2403226	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2403227	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs2403229	0.80[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap]
rs4478985	0.97[ASN][1000 genomes]
rs4529876	0.86[ASN][1000 genomes]
rs4576815	0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs4625455	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs4909917	0.80[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs4910086	0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs57420335	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs59757006	0.90[ASN][1000 genomes]
rs7106914	0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs7114303	0.93[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7121617	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7938788	0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7946995	0.92[CHB][hapmap];0.93[JPT][hapmap];0.97[ASN][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	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv553476	chr11:10024311-10117435	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv430319	chr11:10027543-10711224	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11042604	SBF2	cis	lymphoblastoid	seeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10072400-10101200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:10074000-10089200	Weak transcription	Ovary	ovary
3	chr11:10074000-10098200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr11:10085000-10098200	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr11:10087600-10089600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr11:10087600-10090000	Enhancers	A549	lung
7	chr11:10087600-10090600	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr11:10087800-10097800	Weak transcription	Right Atrium	heart
9	chr11:10088000-10090000	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr11:10088000-10090000	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr11:10088000-10090000	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr11:10088000-10090200	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr11:10088200-10090200	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr11:10088800-10089600	Enhancers	Hela-S3	cervix
15	chr11:10088800-10090000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr11:10088800-10090200	Enhancers	HUES6 Cell Line	embryonic stem cell

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