Variant report

Variant	rs17472989
Chromosome Location	chr15:49424366-49424367
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:49424176-49425089	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:49423792..49428339-chr15:49429632..49433589,5	K562	blood:

Variant related genes	Relation type
COPS2	TF binding region
ENSG00000200120	Chromatin interaction
ENSG00000166200	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11853969	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11854039	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11854557	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11857515	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs11857773	0.84[ASN][1000 genomes]
rs11858814	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];0.84[ASN][1000 genomes]
rs12899422	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12900819	0.88[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap]
rs12900838	0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12901353	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12902096	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12902271	1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12905094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs12905477	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12914876	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs17393761	0.91[CHB][hapmap];0.85[JPT][hapmap];0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs17435932	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1961393	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2289389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2413926	0.85[CEU][hapmap]
rs34562714	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34748066	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36100631	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4774538	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4775794	0.88[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs4775806	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4775808	0.88[AFR][1000 genomes]
rs55979115	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62009762	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs62009834	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71467664	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7164309	0.86[CEU][hapmap]
rs7180168	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7497335	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8029687	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs8043493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs9672848	0.88[AFR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17472989	COPS2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49388800-49434800	Weak transcription	Small Intestine	intestine
2	chr15:49395600-49426400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr15:49398600-49427600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr15:49403000-49434600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:49403400-49440200	Weak transcription	Pancreas	Pancrea
6	chr15:49403600-49432200	Weak transcription	Fetal Stomach	stomach
7	chr15:49403600-49435200	Weak transcription	Aorta	Aorta
8	chr15:49403600-49435200	Weak transcription	Gastric	stomach
9	chr15:49403600-49435400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr15:49403800-49433200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr15:49404800-49425600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr15:49404800-49434600	Weak transcription	Right Ventricle	heart
13	chr15:49404800-49435000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr15:49405600-49441800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr15:49411400-49432200	Weak transcription	Fetal Intestine Small	intestine
16	chr15:49413000-49427200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr15:49413400-49426200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr15:49413600-49447000	Weak transcription	Stomach Mucosa	stomach
19	chr15:49414000-49426400	Strong transcription	HSMM	muscle
20	chr15:49415200-49433400	Weak transcription	Lung	lung
21	chr15:49415400-49427400	Strong transcription	Hela-S3	cervix
22	chr15:49415400-49427600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr15:49415600-49427400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr15:49415600-49437600	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr15:49415800-49437400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr15:49416200-49427600	Weak transcription	Fetal Brain Male	brain
27	chr15:49416200-49437400	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr15:49416400-49427800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr15:49416800-49436800	Strong transcription	Liver	Liver
30	chr15:49416800-49437200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr15:49417000-49437200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr15:49417200-49424400	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr15:49417200-49424800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr15:49417200-49426600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr15:49417200-49436600	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr15:49417200-49437200	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr15:49417200-49437200	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr15:49417200-49437400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr15:49417200-49437400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr15:49417400-49427600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr15:49417400-49427600	Strong transcription	Placenta	Placenta
42	chr15:49417400-49437200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr15:49417600-49437200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr15:49417600-49437200	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr15:49417800-49437200	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr15:49418000-49426200	Strong transcription	HUVEC	blood vessel
47	chr15:49418000-49435800	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr15:49418600-49426800	Strong transcription	Osteobl	bone
49	chr15:49418600-49436000	Strong transcription	Fetal Thymus	thymus
50	chr15:49418600-49437600	Strong transcription	Primary B cells from peripheral blood	blood

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