Variant report

Variant	rs62076549
Chromosome Location	chr17:45579555-45579556
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10048173	0.82[EUR][1000 genomes]
rs11650210	0.85[AFR][1000 genomes]
rs11651766	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11869940	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11870057	0.81[ASN][1000 genomes]
rs12051716	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12103836	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12602134	0.91[EUR][1000 genomes]
rs2085755	0.82[EUR][1000 genomes]
rs35159316	0.91[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4794007	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4794051	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4794058	0.83[ASN][1000 genomes]
rs6504963	0.89[AFR][1000 genomes]
rs7221548	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7222851	0.84[EUR][1000 genomes]
rs72829689	0.81[ASN][1000 genomes]
rs7350906	0.84[EUR][1000 genomes]
rs7405889	0.86[EUR][1000 genomes]
rs8065990	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8074149	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9895274	0.82[EUR][1000 genomes]
rs9897063	0.82[EUR][1000 genomes]
rs9901869	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9903898	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062983	chr17:45030095-45789543	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv516872	chr17:45419139-45702280	Strong transcription Genic enhancers Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv525267	chr17:45451894-45735706	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	esv1806110	chr17:45477544-45673592	Weak transcription Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv908568	chr17:45506682-45590420	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv833468	chr17:45511563-45683164	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv469573	chr17:45511582-45698942	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv471701	chr17:45511583-45698942	Genic enhancers Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	esv1793478	chr17:45518444-45671051	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	esv1811231	chr17:45520374-45764956	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	esv1813964	chr17:45520374-45764956	Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
12	esv2758458	chr17:45520374-45764956	Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
13	esv2758693	chr17:45520374-45764956	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
14	nsv428344	chr17:45520374-45764956	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
15	nsv908569	chr17:45537395-45603094	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
16	esv1808961	chr17:45542951-45664746	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
17	esv33689	chr17:45551959-45664575	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
18	nsv471513	chr17:45552080-45671439	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
19	nsv978433	chr17:45560111-45600707	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
20	nsv908570	chr17:45571502-45684651	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs62076549	KPNB1	Cis_1M	lymphoblastoid	RTeQTL
rs62076549	MRPL45P2	cis	Muscle Skeletal	GTEx
rs62076549	TBKBP1	cis	Nerve Tibial	GTEx
rs62076549	TBKBP1	cis	Artery Tibial	GTEx
rs62076549	SCRN2	cis	lung	GTEx

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45578400-45579800	Enhancers	Placenta	Placenta
2	chr17:45578600-45580200	Enhancers	Fetal Muscle Leg	muscle
3	chr17:45578800-45579600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr17:45578800-45579800	Enhancers	Fetal Intestine Large	intestine
5	chr17:45579000-45579600	Enhancers	Thymus	Thymus
6	chr17:45579000-45579800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr17:45579000-45579800	Flanking Active TSS	Hela-S3	cervix
8	chr17:45579000-45579800	Enhancers	HMEC	breast
9	chr17:45579000-45579800	Enhancers	HSMM	muscle
10	chr17:45579000-45579800	Enhancers	HSMMtube	muscle
11	chr17:45579000-45580200	Enhancers	Fetal Thymus	thymus
12	chr17:45579000-45580600	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr17:45579000-45580600	Enhancers	Dnd41	blood
14	chr17:45579200-45579600	Enhancers	Primary B cells from cord blood	blood
15	chr17:45579200-45579600	Enhancers	Placenta Amnion	Placenta Amnion
16	chr17:45579200-45579800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr17:45579200-45579800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr17:45579200-45579800	Enhancers	Primary hematopoietic stem cells	blood
19	chr17:45579200-45579800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr17:45579200-45579800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr17:45579200-45579800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr17:45579200-45579800	Enhancers	Colon Smooth Muscle	Colon
23	chr17:45579200-45579800	Enhancers	Duodenum Mucosa	Duodenum
24	chr17:45579200-45579800	Enhancers	Fetal Brain Male	brain
25	chr17:45579200-45579800	Enhancers	Fetal Intestine Small	intestine
26	chr17:45579200-45579800	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr17:45579200-45579800	Flanking Active TSS	GM12878-XiMat	blood
28	chr17:45579200-45579800	Flanking Active TSS	HepG2	liver
29	chr17:45579200-45579800	Flanking Active TSS	NHDF-Ad	bronchial
30	chr17:45579200-45580000	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr17:45579200-45580000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr17:45579200-45580000	Enhancers	K562	blood
33	chr17:45579200-45580200	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr17:45579200-45580200	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr17:45579200-45580200	Enhancers	Adipose Nuclei	Adipose
36	chr17:45579200-45580200	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr17:45579200-45580600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr17:45579200-45580600	Enhancers	NHLF	lung
39	chr17:45579200-45581000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr17:45579400-45579600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
41	chr17:45579400-45579800	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr17:45579400-45579800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr17:45579400-45579800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr17:45579400-45579800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr17:45579400-45579800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr17:45579400-45579800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
47	chr17:45579400-45579800	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr17:45579400-45579800	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr17:45579400-45579800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr17:45579400-45579800	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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