Variant report

Variant	rs2287643
Chromosome Location	chr2:54335506-54335507
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54335252..54336789-chr2:54355206..54357354,2	MCF-7	breast:
2	chr2:54334014..54340621-chr2:54341231..54344595,11	MCF-7	breast:
3	chr2:54333529..54340855-chr2:54341009..54344742,14	K562	blood:

Variant related genes	Relation type
ENSG00000170634	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10496028	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1075264	0.90[ASN][1000 genomes]
rs11676462	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11890838	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs11896815	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11898855	0.82[AMR][1000 genomes]
rs17039547	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17045452	0.82[CHB][hapmap]
rs17045474	0.91[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17045488	0.91[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1877907	0.86[ASN][1000 genomes]
rs1877908	0.86[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs2287639	0.89[ASN][1000 genomes]
rs2357896	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2909459	0.82[CHB][hapmap];0.83[JPT][hapmap];0.92[YRI][hapmap]
rs34498089	0.95[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34773403	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4671861	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55649409	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55705819	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56193146	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62137964	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62137976	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62137980	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62140990	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62141002	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6545381	0.80[AMR][1000 genomes]
rs6545386	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6706363	0.87[ASN][1000 genomes]
rs6713088	0.92[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs6714450	0.82[AMR][1000 genomes]
rs6721970	0.95[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6746965	0.84[CHB][hapmap]
rs6751105	0.91[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs7559380	0.87[ASN][1000 genomes]
rs7559384	0.80[AMR][1000 genomes]
rs7565453	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7573551	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7576901	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7590819	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs805310	0.83[CHB][hapmap]
rs805321	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs805328	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs805338	0.92[YRI][hapmap]
rs805351	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs805352	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs805365	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs805446	0.92[YRI][hapmap]
rs805449	0.91[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 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
9	nsv1010175	chr2:54292951-54343466	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	esv1851003	chr2:54324701-54372931	Genic enhancers Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
11	nsv1007731	chr2:54331179-54452329	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
12	nsv535723	chr2:54331179-54452329	Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2287643	PSME4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54291200-54342000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr2:54331200-54342000	Weak transcription	Psoas Muscle	Psoas
3	chr2:54331200-54342400	Weak transcription	Pancreas	Pancrea
4	chr2:54331400-54335800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr2:54331400-54335800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr2:54331400-54342200	Weak transcription	Aorta	Aorta
7	chr2:54333600-54335800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:54333800-54341800	Weak transcription	K562	blood
9	chr2:54334200-54336000	Enhancers	Fetal Brain Male	brain
10	chr2:54334400-54335600	Enhancers	Fetal Kidney	kidney
11	chr2:54334400-54335800	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr2:54334400-54335800	Enhancers	HepG2	liver
13	chr2:54334600-54335600	Flanking Active TSS	Brain Hippocampus Middle	brain
14	chr2:54334600-54335800	Enhancers	HSMM	muscle
15	chr2:54334600-54335800	Enhancers	HSMMtube	muscle
16	chr2:54334600-54336000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr2:54334600-54336000	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr2:54334800-54335600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:54334800-54335600	Flanking Active TSS	Brain Angular Gyrus	brain
20	chr2:54334800-54335600	Flanking Active TSS	Brain Cingulate Gyrus	brain
21	chr2:54334800-54335800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr2:54334800-54335800	Enhancers	Brain Germinal Matrix	brain
23	chr2:54334800-54336000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr2:54334800-54341600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:54334800-54341800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr2:54334800-54342000	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr2:54335000-54335600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr2:54335000-54335800	Weak transcription	Primary B cells from cord blood	blood
29	chr2:54335000-54335800	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr2:54335000-54335800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr2:54335000-54335800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr2:54335000-54335800	Enhancers	Fetal Muscle Leg	muscle
33	chr2:54335000-54336000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr2:54335000-54336000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr2:54335000-54336000	Enhancers	Liver	Liver
36	chr2:54335000-54336000	Enhancers	NHEK	skin
37	chr2:54335200-54335600	Flanking Active TSS	Brain Anterior Caudate	brain
38	chr2:54335200-54335600	Enhancers	Fetal Heart	heart
39	chr2:54335200-54335800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr2:54335200-54336000	Enhancers	HMEC	breast
41	chr2:54335200-54341200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr2:54335400-54335600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr2:54335400-54335600	Flanking Active TSS	Brain Substantia Nigra	brain
44	chr2:54335400-54335800	Enhancers	Fetal Brain Female	brain
45	chr2:54335400-54336000	Enhancers	Primary B cells from peripheral blood	blood

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