Variant report

Variant	rs10439478
Chromosome Location	chr2:54459450-54459451
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	chr2:54457083..54460035-chr2:54464183..54466106,2	K562	blood:

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10165485	0.83[YRI][hapmap];0.84[AFR][1000 genomes]
rs10188489	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10865281	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11125526	0.95[CEU][hapmap];0.86[CHB][hapmap];0.82[EUR][1000 genomes]
rs11125528	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11125529	0.83[YRI][hapmap];0.85[AFR][1000 genomes]
rs11884867	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11886559	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11890390	0.94[YRI][hapmap];0.87[AFR][1000 genomes]
rs11893929	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[EUR][1000 genomes]
rs11894205	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11896604	0.94[YRI][hapmap];0.88[AFR][1000 genomes]
rs11899551	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12612860	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12614774	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12616744	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12616857	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13410397	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[EUR][1000 genomes]
rs13412139	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13417493	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[EUR][1000 genomes]
rs1385273	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.91[EUR][1000 genomes]
rs1399513	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes]
rs1484692	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17045583	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[EUR][1000 genomes]
rs17045585	0.88[EUR][1000 genomes]
rs17045588	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes]
rs17045654	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17045658	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17045688	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17045704	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17045711	0.84[YRI][hapmap];0.85[AFR][1000 genomes]
rs1872329	0.88[YRI][hapmap];0.86[AFR][1000 genomes]
rs1986036	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2010461	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2062341	0.95[YRI][hapmap]
rs28416696	0.87[AFR][1000 genomes]
rs35126790	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3912428	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3915270	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55743218	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56042969	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56755567	0.97[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs58107053	0.90[EUR][1000 genomes]
rs62138037	0.87[EUR][1000 genomes]
rs62139188	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62139253	0.85[AFR][1000 genomes]
rs62139258	0.84[AFR][1000 genomes]
rs6717823	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6723912	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6732970	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72802630	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72802650	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7567646	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7602930	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7607356	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003205	chr2:54220049-54700843	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv2762639	chr2:54220049-54700855	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1002891	chr2:54227005-54682169	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv535722	chr2:54227005-54682169	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv1011690	chr2:54255361-54700843	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv1000652	chr2:54345892-54469703	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv1009828	chr2:54393122-54488721	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv532512	chr2:54453210-54630755	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv457897	chr2:54459093-54502912	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	nsv582012	chr2:54459093-54502912	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54449800-54535200	Weak transcription	Primary T cells from cord blood	blood
2	chr2:54452400-54468000	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr2:54452800-54490200	Weak transcription	Primary B cells from cord blood	blood
4	chr2:54453800-54460400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr2:54453800-54466200	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr2:54455400-54461400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:54455800-54466200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr2:54455800-54476000	Weak transcription	K562	blood
9	chr2:54456400-54460000	Weak transcription	Brain Anterior Caudate	brain
10	chr2:54456400-54466200	Weak transcription	Ovary	ovary
11	chr2:54456400-54487200	Weak transcription	Psoas Muscle	Psoas
12	chr2:54457200-54461400	Weak transcription	Adipose Nuclei	Adipose
13	chr2:54457600-54461000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr2:54458800-54463200	Enhancers	HepG2	liver
15	chr2:54459400-54459600	Enhancers	Esophagus	oesophagus
16	chr2:54459400-54459600	ZNF genes & repeats	HSMM	muscle
17	chr2:54459400-54459800	ZNF genes & repeats	Left Ventricle	heart
18	chr2:54459400-54461400	Weak transcription	Primary hematopoietic stem cells	blood

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