Variant report

Variant	rs4011743
Chromosome Location	chr1:222954347-222954348
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	chr1:222953543..222955080-chr1:222964714..222967533,2	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11490203	0.83[EUR][1000 genomes]
rs11490204	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11490205	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17163484	0.97[ASN][1000 genomes]
rs17474556	0.80[ASN][1000 genomes]
rs17474745	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17533651	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17533810	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17533873	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2378602	0.95[ASN][1000 genomes]
rs2889937	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2889940	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3008634	0.82[CHB][hapmap]
rs34251271	0.97[ASN][1000 genomes]
rs34311160	0.83[EUR][1000 genomes]
rs34430931	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34494528	0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs34643154	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34687048	0.95[ASN][1000 genomes]
rs34807177	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35292789	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35325797	0.95[ASN][1000 genomes]
rs35472374	0.95[ASN][1000 genomes]
rs35554894	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35651802	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35684750	0.91[CHB][hapmap]
rs35762933	0.91[CHB][hapmap]
rs35840203	0.95[ASN][1000 genomes]
rs35976854	0.98[ASN][1000 genomes]
rs3922772	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4240935	0.84[EUR][1000 genomes]
rs4264001	0.97[ASN][1000 genomes]
rs4303078	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4322239	0.95[ASN][1000 genomes]
rs4424514	0.97[ASN][1000 genomes]
rs4472762	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4480364	0.96[ASN][1000 genomes]
rs4562632	0.98[ASN][1000 genomes]
rs61826464	0.95[ASN][1000 genomes]
rs61826465	0.95[ASN][1000 genomes]
rs61826467	0.95[ASN][1000 genomes]
rs61826474	0.97[ASN][1000 genomes]
rs61837141	0.97[ASN][1000 genomes]
rs61837143	0.97[ASN][1000 genomes]
rs61837144	0.90[ASN][1000 genomes]
rs61837145	0.80[ASN][1000 genomes]
rs61837146	0.80[ASN][1000 genomes]
rs61837147	0.97[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	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	esv3369664	chr1:222935606-222958164	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4011743	HHIPL2	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222947200-222959200	Weak transcription	Fetal Brain Male	brain
2	chr1:222948200-222961600	Weak transcription	Primary B cells from cord blood	blood
3	chr1:222951400-222959400	Weak transcription	Stomach Mucosa	stomach
4	chr1:222951600-222959600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:222951800-222956400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:222953400-222968000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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