Variant report

Variant	rs17054790
Chromosome Location	chr13:37562621-37562622
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:37557592..37563683-chr13:37571842..37575220,9	MCF-7	breast:
2	chr13:37559855..37563377-chr13:37569856..37572688,4	K562	blood:
3	chr13:37555502..37557441-chr13:37560771..37563958,3	K562	blood:

Variant related genes	Relation type
ENSG00000120699	Chromatin interaction
ENSG00000120697	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

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]
rs17054789	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]
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];0.90[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];1.00[ASN][1000 genomes]
rs17054838	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[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]
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	0.87[AFR][1000 genomes]
rs9594180	0.95[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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs9603118	0.82[AFR][1000 genomes]
rs9603124	1.00[CEU][hapmap];1.00[CHB][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]

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
rs17054790	PENK	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:37524000-37563800	Weak transcription	Psoas Muscle	Psoas
2	chr13:37524600-37572400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr13:37531800-37570000	Strong transcription	Dnd41	blood
4	chr13:37547400-37570000	Strong transcription	Fetal Thymus	thymus
5	chr13:37547800-37570200	Strong transcription	Primary T helper cells PMA-I stimulated	--
6	chr13:37549000-37569400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr13:37550000-37563800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr13:37550000-37565400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr13:37550400-37570200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr13:37550600-37570400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr13:37551600-37565000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr13:37552200-37570000	Strong transcription	Fetal Muscle Trunk	muscle
13	chr13:37552400-37570000	Strong transcription	Primary T cells from cord blood	blood
14	chr13:37552600-37570200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr13:37553200-37569600	Strong transcription	Placenta	Placenta
16	chr13:37553200-37569800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr13:37553200-37570000	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr13:37554200-37569800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr13:37554400-37569400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr13:37554600-37569800	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr13:37555200-37570200	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr13:37555200-37571200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr13:37555600-37569200	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr13:37555600-37570200	Strong transcription	Liver	Liver
25	chr13:37555600-37570200	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr13:37555600-37570400	Strong transcription	Skeletal Muscle Female	skeletal muscle
27	chr13:37555600-37570400	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr13:37555800-37567200	Weak transcription	Stomach Mucosa	stomach
29	chr13:37555800-37569400	Strong transcription	Adipose Nuclei	Adipose
30	chr13:37555800-37570000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr13:37555800-37570200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr13:37556000-37566600	Strong transcription	Fetal Muscle Leg	muscle
33	chr13:37556200-37569200	Strong transcription	Brain Hippocampus Middle	brain
34	chr13:37556200-37569600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr13:37556200-37569600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr13:37556200-37569800	Strong transcription	Primary B cells from peripheral blood	blood
37	chr13:37556200-37569800	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr13:37556200-37570200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr13:37556400-37563200	Strong transcription	Colon Smooth Muscle	Colon
40	chr13:37556400-37569600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr13:37556400-37569600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr13:37556400-37569600	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr13:37556400-37569600	Strong transcription	Fetal Lung	lung
44	chr13:37556400-37570000	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr13:37556400-37570200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr13:37556400-37570200	Strong transcription	HSMM	muscle
47	chr13:37556400-37570400	Strong transcription	Primary B cells from cord blood	blood
48	chr13:37556400-37570400	Strong transcription	Duodenum Mucosa	Duodenum
49	chr13:37556600-37569800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr13:37556600-37570200	Strong transcription	Stomach Smooth Muscle	stomach

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