Variant report

Variant	rs17039547
Chromosome Location	chr2:54333729-54333730
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	chr2:54333529..54340855-chr2:54341009..54344742,14	K562	blood:

Variant related genes	Relation type
ENSG00000170634	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10183655	0.81[CHD][hapmap]
rs10496028	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1075264	0.90[ASN][1000 genomes]
rs11676462	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11890838	0.86[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap]
rs11896815	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11898855	0.80[AMR][1000 genomes]
rs17045452	0.83[CHD][hapmap];0.80[GIH][hapmap];0.86[MEX][hapmap]
rs17045474	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17045488	0.91[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1877907	0.86[ASN][1000 genomes]
rs1877908	0.91[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs2287639	0.89[ASN][1000 genomes]
rs2287643	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]
rs2357896	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2909459	0.82[JPT][hapmap];0.92[YRI][hapmap]
rs34498089	0.89[ASW][hapmap];0.95[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.80[MEX][hapmap];0.88[MKK][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34773403	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3731967	0.83[CHD][hapmap];0.85[GIH][hapmap]
rs4671861	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55649409	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55705819	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56193146	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62137964	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62137976	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62137980	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62140990	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62141002	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6545386	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6706363	0.87[ASN][1000 genomes]
rs6713088	0.95[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs6714450	0.80[AMR][1000 genomes]
rs6721970	0.89[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.83[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6751105	0.95[CHB][hapmap];0.88[CHD][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs7559380	0.87[ASN][1000 genomes]
rs7565453	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7573551	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7576901	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7590819	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs805316	0.92[LWK][hapmap];0.84[YRI][hapmap]
rs805321	0.89[JPT][hapmap]
rs805328	0.94[JPT][hapmap]
rs805338	0.92[YRI][hapmap]
rs805351	0.89[JPT][hapmap]
rs805352	0.82[ASW][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap]
rs805365	0.82[ASW][hapmap];0.84[CHD][hapmap];0.93[GIH][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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17039547	PRDXDD1P	cis	parietal	SCAN
rs17039547	ACYP2	cis	multi-tissue	Pritchard
rs17039547	PSME4	cis	lymphoblastoid	seeQTL
rs17039547	PSME4	cis	cerebellum	SCAN
rs17039547	MTIF2	cis	cerebellum	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54291200-54342000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr2:54324000-54334400	Enhancers	Primary B cells from peripheral blood	blood
3	chr2:54325800-54334400	Weak transcription	Brain Angular Gyrus	brain
4	chr2:54326000-54334000	Weak transcription	Brain Substantia Nigra	brain
5	chr2:54331200-54335000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:54331200-54342000	Weak transcription	Psoas Muscle	Psoas
7	chr2:54331200-54342400	Weak transcription	Pancreas	Pancrea
8	chr2:54331400-54334000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr2:54331400-54334000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr2:54331400-54334000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr2:54331400-54334000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr2:54331400-54334000	Weak transcription	Brain Anterior Caudate	brain
13	chr2:54331400-54334000	Weak transcription	Brain Hippocampus Middle	brain
14	chr2:54331400-54334000	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr2:54331400-54334000	Weak transcription	Thymus	Thymus
16	chr2:54331400-54334000	Weak transcription	HSMMtube	muscle
17	chr2:54331400-54334400	Weak transcription	Adipose Nuclei	Adipose
18	chr2:54331400-54334400	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr2:54331400-54334600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr2:54331400-54334800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:54331400-54334800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr2:54331400-54335000	Weak transcription	Fetal Muscle Leg	muscle
23	chr2:54331400-54335200	Weak transcription	Fetal Heart	heart
24	chr2:54331400-54335400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr2:54331400-54335800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr2:54331400-54335800	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr2:54331400-54342200	Weak transcription	Aorta	Aorta
28	chr2:54331600-54334000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:54331600-54334000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr2:54331600-54334200	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr2:54331600-54334200	Weak transcription	HUVEC	blood vessel
32	chr2:54331600-54334600	Weak transcription	NHDF-Ad	bronchial
33	chr2:54331600-54335000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr2:54331800-54334000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr2:54331800-54334400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr2:54331800-54335000	Weak transcription	NHEK	skin
37	chr2:54332000-54333800	Weak transcription	HepG2	liver
38	chr2:54332000-54334000	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr2:54332000-54334200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr2:54332000-54335200	Weak transcription	HMEC	breast
41	chr2:54332200-54334000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr2:54332400-54334000	Weak transcription	Hela-S3	cervix
43	chr2:54332400-54334800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr2:54332400-54335000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr2:54333400-54333800	Weak transcription	Primary B cells from cord blood	blood
46	chr2:54333600-54333800	Enhancers	Liver	Liver
47	chr2:54333600-54333800	Enhancers	K562	blood
48	chr2:54333600-54334200	Enhancers	A549	lung
49	chr2:54333600-54335800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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