Variant report

Variant	rs11890838
Chromosome Location	chr2:54261066-54261067
allele	C/T
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	STAT3	chr2:54260834-54261186	MCF10A-Er-Src	breast:	n/a	chr2:54261023-54261031 chr2:54261051-54261060 chr2:54261020-54261034 chr2:54261021-54261032 chr2:54261017-54261037
2	FOS	chr2:54260911-54261199	MCF10A-Er-Src	breast:	n/a	chr2:54261050-54261061
3	STAT3	chr2:54260775-54261211	MCF10A-Er-Src	breast:	n/a	chr2:54261023-54261031 chr2:54261051-54261060 chr2:54261020-54261034 chr2:54261021-54261032 chr2:54261017-54261037
4	FOS	chr2:54260920-54261187	MCF10A-Er-Src	breast:	n/a	chr2:54261050-54261061
5	FOS	chr2:54260927-54261213	HUVEC	blood vessel:	n/a	chr2:54261050-54261061
6	FOS	chr2:54260901-54261179	MCF10A-Er-Src	breast:	n/a	chr2:54261050-54261061
7	STAT3	chr2:54260890-54261186	MCF10A-Er-Src	breast:	n/a	chr2:54261023-54261031 chr2:54261051-54261060 chr2:54261020-54261034 chr2:54261021-54261032 chr2:54261017-54261037

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ACYP2-4	chr2:54259644-54261288	NONHSAT070722

Variant related genes	Relation type
ENSG00000235937	TF binding region

Extended variants
information (count: 85 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10084374	0.89[ASN][1000 genomes]
rs10167891	0.84[ASN][1000 genomes]
rs10181999	0.91[ASN][1000 genomes]
rs10183655	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs10186566	0.83[ASN][1000 genomes]
rs10496028	0.81[ASN][1000 genomes]
rs11674724	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11676462	0.89[ASN][1000 genomes]
rs11683741	0.84[EUR][1000 genomes]
rs11689025	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11893270	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11896815	0.92[ASN][1000 genomes]
rs11898855	0.94[ASN][1000 genomes]
rs13394278	0.82[ASN][1000 genomes]
rs1477258	0.81[ASN][1000 genomes]
rs17039547	0.86[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap]
rs17045452	0.85[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs17045474	0.95[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs17045488	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1877908	0.86[CHD][hapmap]
rs2112122	0.87[ASN][1000 genomes]
rs2287643	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs2357896	0.93[ASN][1000 genomes]
rs28653587	0.82[ASN][1000 genomes]
rs28851028	0.83[ASN][1000 genomes]
rs2909459	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs2949815	0.80[EUR][1000 genomes]
rs34498089	0.88[CHD][hapmap];0.84[JPT][hapmap]
rs34773403	0.85[ASN][1000 genomes]
rs3731967	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs4671746	0.85[ASN][1000 genomes]
rs4671747	0.80[ASN][1000 genomes]
rs55649409	0.92[ASN][1000 genomes]
rs55692047	0.87[ASN][1000 genomes]
rs55705819	0.81[ASN][1000 genomes]
rs56302494	0.86[ASN][1000 genomes]
rs62140990	0.86[ASN][1000 genomes]
rs62141002	0.86[ASN][1000 genomes]
rs6545377	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6545380	0.83[ASN][1000 genomes]
rs6545381	0.95[ASN][1000 genomes]
rs6711105	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6711217	0.87[ASN][1000 genomes]
rs6713088	0.81[CHB][hapmap]
rs6714450	0.96[ASN][1000 genomes]
rs6715488	0.85[ASN][1000 genomes]
rs6721970	0.87[CHB][hapmap]
rs6743455	0.91[ASN][1000 genomes]
rs6746965	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs6748976	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6748997	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6751105	0.81[CHB][hapmap];0.83[CHD][hapmap]
rs698855	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs72799298	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7559384	0.96[ASN][1000 genomes]
rs7559947	0.83[EUR][1000 genomes]
rs7564912	0.82[ASN][1000 genomes]
rs7573551	0.81[ASN][1000 genomes]
rs7576901	0.86[ASN][1000 genomes]
rs7590819	0.86[ASN][1000 genomes]
rs7591431	0.82[ASN][1000 genomes]
rs805310	0.85[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs805321	0.91[CHB][hapmap]
rs805328	0.90[CHB][hapmap];0.83[JPT][hapmap];0.81[YRI][hapmap]
rs805334	1.00[YRI][hapmap]
rs805344	0.83[EUR][1000 genomes]
rs805351	0.91[CHB][hapmap];0.81[YRI][hapmap]
rs805352	0.91[CHB][hapmap];0.83[CHD][hapmap];0.81[YRI][hapmap]
rs805365	0.91[CHB][hapmap];0.83[CHD][hapmap];0.81[YRI][hapmap]
rs805386	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs805399	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs805401	0.91[CHB][hapmap]
rs805404	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs805408	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs805426	0.91[CHB][hapmap]
rs805447	1.00[YRI][hapmap]
rs9631059	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001246	chr2:54195654-54434832	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
8	nsv431069	chr2:54260132-54434049	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11890838	PSME4	cis	lymphoblastoid	seeQTL
rs11890838	PSME4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54243800-54268000	Weak transcription	Osteobl	bone
2	chr2:54243800-54268400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr2:54243800-54269800	Weak transcription	Brain Anterior Caudate	brain
4	chr2:54246800-54275200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:54248600-54278000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr2:54248600-54289800	Weak transcription	Fetal Lung	lung
7	chr2:54248800-54275600	Weak transcription	Primary B cells from cord blood	blood
8	chr2:54251600-54263800	Weak transcription	Primary T cells from cord blood	blood
9	chr2:54254600-54267400	Weak transcription	Brain Substantia Nigra	brain
10	chr2:54254600-54269800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr2:54254800-54269600	Weak transcription	Colon Smooth Muscle	Colon
12	chr2:54258000-54272200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr2:54258200-54264400	Weak transcription	Fetal Brain Female	brain
14	chr2:54258200-54266200	Weak transcription	Fetal Intestine Small	intestine
15	chr2:54258200-54266400	Weak transcription	Psoas Muscle	Psoas
16	chr2:54258200-54267000	Weak transcription	Ovary	ovary
17	chr2:54258200-54269600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr2:54258200-54269800	Weak transcription	Fetal Heart	heart
19	chr2:54258200-54269800	Weak transcription	Fetal Muscle Leg	muscle
20	chr2:54258200-54270000	Weak transcription	HepG2	liver
21	chr2:54259000-54267200	Weak transcription	Adipose Nuclei	Adipose
22	chr2:54260000-54269800	Weak transcription	Stomach Smooth Muscle	stomach
23	chr2:54260000-54272200	Weak transcription	Primary B cells from peripheral blood	blood
24	chr2:54260400-54278200	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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