Variant report

Variant	rs4459557
Chromosome Location	chr16:31361643-31361644
allele	C/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	RUNX3	chr16:31361556-31361977	GM12878	blood:	n/a	n/a
2	CTCF	chr16:31361560-31361710	GM12873	blood:	n/a	n/a
3	MAX	chr16:31361604-31361969	NB4	blood:	n/a	n/a
4	RUNX3	chr16:31361586-31362254	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:31360184..31362565-chr16:31363360..31366821,3	MCF-7	breast:
2	chr16:31360694..31362318-chr16:31366336..31368356,2	K562	blood:

Variant related genes	Relation type
ITGAX	TF binding region
ENSG00000140678	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10747210	0.97[ASN][1000 genomes]
rs10782004	0.93[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs1106398	0.93[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs11150610	0.93[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs11150611	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11150612	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11150613	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11150614	0.95[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11150616	0.90[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11150617	0.83[ASN][1000 genomes]
rs11150619	0.90[JPT][hapmap]
rs1143682	0.93[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs11574630	0.93[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs11574631	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11574639	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11641202	0.86[ASN][1000 genomes]
rs11642120	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11645526	0.86[CHB][hapmap]
rs11645917	0.99[ASN][1000 genomes]
rs11859274	0.99[ASN][1000 genomes]
rs11863627	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12597154	0.89[ASN][1000 genomes]
rs12600286	0.92[ASN][1000 genomes]
rs12923297	0.93[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12935192	0.99[ASN][1000 genomes]
rs13332545	0.95[JPT][hapmap]
rs13338928	0.90[ASN][1000 genomes]
rs2011491	0.81[EUR][1000 genomes]
rs2359661	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs28372932	0.88[ASN][1000 genomes]
rs3087796	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36100148	0.91[ASN][1000 genomes]
rs3764327	0.86[CHB][hapmap]
rs3815801	0.86[CHB][hapmap]
rs3925074	0.94[ASN][1000 genomes]
rs3925075	0.94[ASN][1000 genomes]
rs4075052	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4077810	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41440449	0.88[ASN][1000 genomes]
rs4261553	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4280256	0.80[ASN][1000 genomes]
rs4359460	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4411512	0.93[ASN][1000 genomes]
rs4448960	0.94[ASN][1000 genomes]
rs4450409	0.85[ASN][1000 genomes]
rs4493054	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4506917	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4594268	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4597342	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4608351	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4889543	0.89[ASN][1000 genomes]
rs4889640	0.86[CHB][hapmap]
rs4889647	0.85[ASN][1000 genomes]
rs4889649	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs55742763	0.89[ASN][1000 genomes]
rs55912556	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56392848	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57202326	0.86[ASN][1000 genomes]
rs59338016	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61194152	0.94[ASN][1000 genomes]
rs62051517	0.91[ASN][1000 genomes]
rs6565225	0.83[EUR][1000 genomes]
rs7190997	0.86[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs7192161	0.85[ASN][1000 genomes]
rs7192375	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7193943	0.86[CHB][hapmap]
rs7195915	0.91[ASN][1000 genomes]
rs7195945	0.91[ASN][1000 genomes]
rs7203472	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7206295	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7499192	0.82[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs7501207	0.82[ASN][1000 genomes]
rs8048583	0.93[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs8052324	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8057320	0.86[CHB][hapmap]
rs8058882	0.86[ASN][1000 genomes]
rs8060268	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8062159	0.86[ASN][1000 genomes]
rs929868	0.81[EUR][1000 genomes]
rs9673398	0.93[ASN][1000 genomes]
rs9673404	0.92[ASN][1000 genomes]
rs9673405	0.94[ASN][1000 genomes]
rs9673519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9673522	0.94[ASN][1000 genomes]
rs9674009	0.94[ASN][1000 genomes]
rs9888907	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059459	chr16:31299088-31462251	Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv542901	chr16:31299088-31462251	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv3392534	chr16:31303038-31573066	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	104 gene(s)	inside rSNPs	diseases
4	nsv1058992	chr16:31337455-31414881	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv542902	chr16:31337455-31414881	Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv1061980	chr16:31338462-31415471	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv833194	chr16:31358179-31528545	Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4459557	PYDC1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31343000-31400800	Weak transcription	Right Atrium	heart
2	chr16:31355600-31365600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr16:31356600-31363600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr16:31358000-31362800	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr16:31358600-31366400	Enhancers	Primary B cells from peripheral blood	blood
6	chr16:31358800-31362800	Enhancers	GM12878-XiMat	blood
7	chr16:31358800-31366000	Enhancers	Primary hematopoietic stem cells	blood
8	chr16:31359000-31363200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr16:31359000-31365600	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr16:31359400-31362800	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr16:31359600-31362000	Enhancers	Spleen	Spleen
12	chr16:31359600-31363400	Enhancers	Primary B cells from cord blood	blood
13	chr16:31359800-31363400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr16:31360000-31361800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr16:31360400-31363600	Weak transcription	Fetal Muscle Leg	muscle
16	chr16:31361200-31363400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr16:31361200-31368000	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr16:31361400-31362000	Weak transcription	Adipose Nuclei	Adipose
19	chr16:31361600-31361800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr16:31361600-31362000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
21	chr16:31361600-31362000	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr16:31361600-31362200	Enhancers	Primary T killer memory cells from peripheral blood	blood

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