Variant report

Variant	rs17054789
Chromosome Location	chr13:37561187-37561188
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:37560675..37562585-chr13:37574399..37576736,2	K562	blood:
2	chr13:37557592..37563683-chr13:37571842..37575220,9	MCF-7	breast:
3	chr13:37559041..37561976-chr13:37572718..37575249,3	MCF-7	breast:
4	chr13:37559855..37563377-chr13:37569856..37572688,4	K562	blood:
5	chr13:37555502..37557441-chr13:37560771..37563958,3	K562	blood:
6	chr13:37396258..37399130-chr13:37559801..37562169,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000120697	Chromatin interaction
ENSG00000120699	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10507444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1199997	1.00[ASN][1000 genomes]
rs1199998	1.00[ASN][1000 genomes]
rs1200000	1.00[ASN][1000 genomes]
rs1200001	1.00[ASN][1000 genomes]
rs1200002	1.00[ASN][1000 genomes]
rs1200003	1.00[ASN][1000 genomes]
rs1336165	1.00[ASN][1000 genomes]
rs17054770	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17054775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17054790	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17054792	0.84[AFR][1000 genomes]
rs17054829	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17054835	0.93[YRI][hapmap];0.83[AFR][1000 genomes]
rs17054838	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];1.00[ASN][1000 genomes]
rs17054925	1.00[ASN][1000 genomes]
rs17054972	1.00[ASN][1000 genomes]
rs1924421	1.00[ASN][1000 genomes]
rs2181788	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs2769542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[TSI][hapmap]
rs4624036	1.00[ASN][1000 genomes]
rs57719094	1.00[ASN][1000 genomes]
rs59899061	1.00[ASN][1000 genomes]
rs59901477	1.00[ASN][1000 genomes]
rs608385	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6563506	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs73533924	1.00[ASN][1000 genomes]
rs73543820	1.00[ASN][1000 genomes]
rs74045176	0.84[AFR][1000 genomes]
rs8001410	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9547703	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs9547704	1.00[CHB][hapmap]
rs9594177	0.98[AFR][1000 genomes]
rs9594180	0.87[AFR][1000 genomes]
rs9594184	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9603124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948975	chr13:37281203-38280430	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv522336	chr13:37305641-37584838	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17054789	PENK	trans	brain	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:37519600-37561400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr13:37524000-37563800	Weak transcription	Psoas Muscle	Psoas
3	chr13:37524600-37572400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr13:37531800-37570000	Strong transcription	Dnd41	blood
5	chr13:37539400-37562400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr13:37539600-37562400	Weak transcription	Fetal Brain Male	brain
7	chr13:37540200-37561400	Weak transcription	Esophagus	oesophagus
8	chr13:37540200-37562200	Weak transcription	K562	blood
9	chr13:37545600-37561200	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr13:37547400-37570000	Strong transcription	Fetal Thymus	thymus
11	chr13:37547800-37570200	Strong transcription	Primary T helper cells PMA-I stimulated	--
12	chr13:37549000-37569400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr13:37550000-37561200	Weak transcription	A549	lung
14	chr13:37550000-37563800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr13:37550000-37565400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr13:37550400-37570200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr13:37550600-37570400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr13:37551600-37565000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr13:37552200-37570000	Strong transcription	Fetal Muscle Trunk	muscle
20	chr13:37552400-37570000	Strong transcription	Primary T cells from cord blood	blood
21	chr13:37552600-37570200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr13:37553200-37569600	Strong transcription	Placenta	Placenta
23	chr13:37553200-37569800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr13:37553200-37570000	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr13:37554200-37561600	Weak transcription	HSMMtube	muscle
26	chr13:37554200-37569800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr13:37554400-37569400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr13:37554600-37569800	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr13:37555200-37570200	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr13:37555200-37571200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr13:37555600-37569200	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr13:37555600-37570200	Strong transcription	Liver	Liver
33	chr13:37555600-37570200	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr13:37555600-37570400	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr13:37555600-37570400	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr13:37555800-37567200	Weak transcription	Stomach Mucosa	stomach
37	chr13:37555800-37569400	Strong transcription	Adipose Nuclei	Adipose
38	chr13:37555800-37570000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr13:37555800-37570200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr13:37556000-37566600	Strong transcription	Fetal Muscle Leg	muscle
41	chr13:37556200-37569200	Strong transcription	Brain Hippocampus Middle	brain
42	chr13:37556200-37569600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr13:37556200-37569600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr13:37556200-37569800	Strong transcription	Primary B cells from peripheral blood	blood
45	chr13:37556200-37569800	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr13:37556200-37570200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr13:37556400-37561400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr13:37556400-37563200	Strong transcription	Colon Smooth Muscle	Colon
49	chr13:37556400-37569600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr13:37556400-37569600	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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