Variant report

Variant	rs12956553
Chromosome Location	chr18:39531129-39531130
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	IRF1	chr18:39530771-39531193	K562	blood:	n/a	chr18:39531022-39531033 chr18:39531022-39531032 chr18:39531023-39531034 chr18:39531022-39531036

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:39527112..39531419-chr18:39531831..39536348,5	K562	blood:
2	chr18:39528858..39531419-chr18:39533035..39536390,4	K562	blood:

Variant related genes	Relation type
PIK3C3	TF binding region
ENSG00000078142	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10502776	0.84[ASN][1000 genomes]
rs11082256	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12605021	0.83[ASN][1000 genomes]
rs12606434	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12607810	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12953847	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12954899	0.83[EUR][1000 genomes]
rs12957030	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12961563	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12962602	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12962732	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1544260	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16960213	0.84[ASN][1000 genomes]
rs16975459	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16975462	0.85[ASN][1000 genomes]
rs28438873	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28541909	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28708684	0.84[ASN][1000 genomes]
rs35269653	0.81[EUR][1000 genomes]
rs35617320	0.80[EUR][1000 genomes]
rs3813065	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3819162	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4121817	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4513183	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55971157	0.82[ASN][1000 genomes]
rs56680148	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61682064	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62082292	0.81[EUR][1000 genomes]
rs67084667	0.80[AMR][1000 genomes]
rs7230624	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7230883	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs7233661	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7237737	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7237780	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7237783	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7238178	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7239652	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7240218	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7241401	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7242727	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73454598	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs8087875	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8092954	0.87[EUR][1000 genomes]
rs8095411	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9949409	0.83[ASN][1000 genomes]
rs9949895	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9954624	0.85[ASN][1000 genomes]
rs9956832	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9958749	0.83[ASN][1000 genomes]
rs9964331	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9965466	0.85[ASN][1000 genomes]
rs9966146	0.84[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	nsv1066869	chr18:38742896-39680723	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv543685	chr18:38742896-39680723	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv949609	chr18:39126941-40070286	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers 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	11 gene(s)	inside rSNPs	diseases
4	nsv431979	chr18:39255558-39696452	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1066029	chr18:39322920-39623625	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv543686	chr18:39322920-39623625	Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv909566	chr18:39327962-39688452	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
8	esv34153	chr18:39398768-39872265	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS 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	9 gene(s)	inside rSNPs	diseases
9	nsv909567	chr18:39470190-39652939	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
10	nsv2268	chr18:39487042-39531721	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
11	nsv909568	chr18:39491873-39768746	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:39524600-39535200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr18:39526600-39535600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr18:39529000-39534400	Weak transcription	GM12878-XiMat	blood
4	chr18:39529200-39534600	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr18:39529200-39534800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr18:39529400-39534400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr18:39529400-39534400	Weak transcription	K562	blood
8	chr18:39529400-39534600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr18:39529400-39534800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr18:39530800-39534600	Weak transcription	Pancreatic Islets	Pancreatic Islet

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