Variant report

Variant	rs11043229
Chromosome Location	chr12:122320400-122320401
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:122319850..122323065-chr12:122324628..122326672,4	MCF-7	breast:
2	chr12:122319572..122322353-chr12:122324355..122326595,2	MCF-7	breast:
3	chr12:122233528..122236149-chr12:122319048..122321732,2	K562	blood:
4	chr12:122238851..122242892-chr12:122319516..122321765,3	MCF-7	breast:
5	chr12:122320221..122322912-chr12:122324691..122327698,3	K562	blood:

Variant related genes	Relation type
ENSG00000272849	Chromatin interaction
ENSG00000139718	Chromatin interaction
ENSG00000256950	Chromatin interaction
ENSG00000139725	Chromatin interaction
ENSG00000110801	Chromatin interaction
ENSG00000212694	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10431199	0.81[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs10840624	0.83[CHB][hapmap]
rs11043216	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs11043218	0.91[CHB][hapmap]
rs11043237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11043242	0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11043255	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11043276	1.00[MEX][hapmap]
rs11043285	0.81[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs11043286	0.81[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap]
rs11615980	0.94[ASN][1000 genomes]
rs12229068	0.89[AFR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1610041	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs2707058	1.00[CEU][hapmap];0.87[CHD][hapmap]
rs35892692	0.97[ASN][1000 genomes]
rs3847694	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3887885	0.97[ASN][1000 genomes]
rs4069668	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap]
rs61954311	0.97[ASN][1000 genomes]
rs6486780	0.97[ASN][1000 genomes]
rs7137218	0.83[CHB][hapmap]
rs7137708	0.85[GIH][hapmap]
rs7139277	1.00[MEX][hapmap]
rs7309024	0.97[ASN][1000 genomes]
rs7313252	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7958406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7969671	0.80[ASN][1000 genomes]
rs7969846	1.00[YRI][hapmap]
rs7970565	0.97[ASN][1000 genomes]
rs7971538	0.81[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv899568	chr12:122254713-122456524	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	esv34001	chr12:122298737-122521637	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11043229	CXCR4	trans	brain	seeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122311000-122320400	Weak transcription	K562	blood
2	chr12:122311800-122321000	Weak transcription	Right Atrium	heart
3	chr12:122312000-122322800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr12:122314600-122320800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:122319400-122321000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:122320000-122321000	Enhancers	HepG2	liver
7	chr12:122320000-122321800	Enhancers	Liver	Liver
8	chr12:122320400-122322000	Enhancers	K562	blood

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