Variant report

Variant	rs6818178
Chromosome Location	chr4:53724744-53724745
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:53723992..53727784-chr4:53728716..53731112,4	K562	blood:
2	chr4:53583825..53585724-chr4:53723633..53725976,2	K562	blood:
3	chr4:53577122..53581435-chr4:53720877..53725671,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226950	Chromatin interaction
ENSG00000128045	Chromatin interaction
ENSG00000212588	Chromatin interaction
ENSG00000264585	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10517269	0.85[CHB][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes]
rs1109696	0.89[YRI][hapmap]
rs11932601	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs11938159	0.82[CHB][hapmap];0.85[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs11939448	0.85[CHB][hapmap];0.85[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs17082074	0.80[ASN][1000 genomes]
rs17082084	0.81[YRI][hapmap]
rs17082087	0.82[AMR][1000 genomes]
rs17082091	0.87[AMR][1000 genomes]
rs2007936	0.89[YRI][hapmap]
rs2007959	0.89[YRI][hapmap]
rs3811781	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs41279517	0.95[ASN][1000 genomes]
rs58461944	0.82[AMR][1000 genomes]
rs58577680	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs59042894	0.87[AMR][1000 genomes]
rs6554054	0.89[AMR][1000 genomes]
rs6554057	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6817433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6838718	0.92[ASW][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6848200	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6858566	0.85[YRI][hapmap]
rs73814868	0.91[AMR][1000 genomes]
rs73814875	0.90[ASN][1000 genomes]
rs73814883	0.95[ASN][1000 genomes]
rs73814886	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7655781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7663419	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7670068	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7685816	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7688141	1.00[CEU][hapmap];0.82[JPT][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7693568	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7699960	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs881744	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv594201	chr4:52798624-53732445	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv1004086	chr4:53698581-53773183	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6818178	CR2	trans	lymphoblastoid	seeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53719800-53727400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:53719800-53727400	Weak transcription	Ovary	ovary
3	chr4:53720600-53727800	Weak transcription	Aorta	Aorta
4	chr4:53720600-53728000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:53721400-53726000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr4:53722200-53725800	Weak transcription	Fetal Brain Male	brain
7	chr4:53722400-53727400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr4:53722400-53727600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr4:53723400-53727200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr4:53723600-53727600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr4:53723800-53724800	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
12	chr4:53723800-53725400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell

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