Variant report

Variant	rs13009889
Chromosome Location	chr2:190628568-190628569
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:190627030-190628574	GM18505	blood:	n/a	n/a
2	POLR2A	chr2:190627247-190629363	K562	blood:	n/a	n/a
3	POLR2A	chr2:190626991-190629517	MCF10A-Er-Src	breast:	n/a	n/a
4	GABPA	chr2:190626855-190628596	MCF-7	breast:	n/a	n/a
5	MXI1	chr2:190626472-190628790	SK-N-SH	brain:	n/a	chr2:190627289-190627298
6	POLR2A	chr2:190626742-190629362	GM12878	blood:	n/a	n/a
7	RFX5	chr2:190628562-190628734	HepG2	liver:	n/a	n/a
8	POLR2A	chr2:190626813-190629360	GM12891	blood:	n/a	n/a
9	CTCF	chr2:190628560-190628710	AG09319	gingival:	n/a	n/a
10	POLR2A	chr2:190628556-190628733	HepG2	liver:	n/a	n/a
11	CTCF	chr2:190626924-190628612	A549	lung:	n/a	chr2:190628388-190628397 chr2:190627929-190627942
12	POLR2A	chr2:190626779-190628772	GM12878	blood:	n/a	n/a
13	POLR2A	chr2:190627067-190629472	Hela-S3	cervix:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:190626375..190630628-chr2:190647839..190651386,6	MCF-7	breast:
2	chr2:190524928..190526526-chr2:190626361..190628930,2	MCF-7	breast:
3	chr2:190524327..190528986-chr2:190625993..190629803,6	K562	blood:
4	chr2:190624834..190631096-chr2:190647637..190651740,7	K562	blood:
5	chr2:190525941..190528751-chr2:190627393..190630465,6	K562	blood:
6	chr2:190626523..190630050-chr2:190647058..190650887,5	MCF-7	breast:
7	chr2:190624834..190630334-chr2:190647529..190650706,8	K562	blood:

No data

Variant related genes	Relation type
OSGEPL1	TF binding region
ENSG00000138381	Chromatin interaction
ENSG00000064933	Chromatin interaction
ENSG00000128699	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10197331	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10207346	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10210345	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1055091	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10931430	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10931431	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10931433	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1132360	0.83[EUR][1000 genomes]
rs11679767	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11685425	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1233245	0.83[EUR][1000 genomes]
rs1233262	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1233265	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1233272	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1233282	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233284	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233288	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233291	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233297	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1233299	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1233302	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1234834	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12471217	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12693551	0.84[EUR][1000 genomes]
rs12693557	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12990627	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12992061	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13002216	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13011710	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13026135	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13035966	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1437891	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1899025	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2017410	0.82[EUR][1000 genomes]
rs2033746	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2033870	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2164832	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2289226	0.83[EUR][1000 genomes]
rs3816196	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4525728	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4667297	0.84[EUR][1000 genomes]
rs4667299	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5742938	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6738042	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6741074	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6942	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7571089	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7591929	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7592066	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7595020	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs893784	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs920427	0.80[EUR][1000 genomes]

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs13009889	ORMDL1	cis	Muscle Skeletal	GTEx
rs13009889	ORMDL1	cis	Adipose Subcutaneous	GTEx
rs13009889	ORMDL1	cis	Heart Left Ventricle	GTEx
rs13009889	ORMDL1	cis	Artery Tibial	GTEx
rs13009889	ORMDL1	cis	Skin Sun Exposed Lower leg	GTEx
rs13009889	ASNSD1	cis	Esophagus Muscularis	GTEx
rs13009889	ASNSD1	cis	Whole Blood	GTEx
rs13009889	PMS1	Cis_1M	lymphoblastoid	RTeQTL
rs13009889	ORMDL1	Cis_1M	lymphoblastoid	RTeQTL
rs13009889	ASNSD1	cis	Nerve Tibial	GTEx
rs13009889	ASNSD1	cis	Artery Tibial	GTEx
rs13009889	ASNSD1	cis	Thyroid	GTEx
rs13009889	ASNSD1	cis	Artery Aorta	GTEx
rs13009889	ASNSD1	Cis_1M	lymphoblastoid	RTeQTL
rs13009889	ORMDL1	cis	Nerve Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190626000-190628600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr2:190626200-190628600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:190626400-190628600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:190626400-190628600	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr2:190626400-190628800	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr2:190626600-190628600	Active TSS	H1 Cell Line	embryonic stem cell
7	chr2:190626600-190628600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr2:190626600-190628600	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr2:190626600-190628600	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr2:190626600-190628600	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr2:190626600-190628800	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr2:190626800-190628600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:190626800-190628600	Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr2:190626800-190628600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
15	chr2:190626800-190628600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr2:190626800-190628600	Active TSS	Fetal Lung	lung
17	chr2:190626800-190628600	Active TSS	Psoas Muscle	Psoas
18	chr2:190626800-190628600	Active TSS	Right Atrium	heart
19	chr2:190626800-190628600	Active TSS	Stomach Smooth Muscle	stomach
20	chr2:190626800-190628600	Active TSS	Hela-S3	cervix
21	chr2:190626800-190628800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr2:190626800-190629000	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr2:190627000-190628600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:190627000-190628600	Active TSS	Aorta	Aorta
25	chr2:190627200-190628600	Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr2:190627200-190628600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr2:190627200-190628600	Active TSS	NHLF	lung
28	chr2:190627800-190629000	Active TSS	Fetal Brain Male	brain
29	chr2:190627800-190642800	Weak transcription	Spleen	Spleen
30	chr2:190627800-190648200	Weak transcription	Gastric	stomach
31	chr2:190628000-190628600	Flanking Active TSS	Primary B cells from cord blood	blood
32	chr2:190628200-190628600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr2:190628200-190628600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:190628200-190628600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr2:190628200-190628600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
36	chr2:190628200-190628600	Flanking Active TSS	Primary B cells from peripheral blood	blood
37	chr2:190628200-190628600	Flanking Active TSS	Primary T cells from cord blood	blood
38	chr2:190628200-190628600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr2:190628200-190628600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
40	chr2:190628200-190628600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
41	chr2:190628200-190628600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
42	chr2:190628200-190628600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr2:190628200-190628600	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr2:190628200-190628600	Flanking Active TSS	Liver	Liver
45	chr2:190628200-190628600	Flanking Active TSS	Duodenum Mucosa	Duodenum
46	chr2:190628200-190628600	Flanking Active TSS	Fetal Brain Female	brain
47	chr2:190628200-190628600	Flanking Active TSS	Fetal Intestine Small	intestine
48	chr2:190628200-190628600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
49	chr2:190628200-190628600	Enhancers	Small Intestine	intestine
50	chr2:190628200-190628600	Flanking Active TSS	HUVEC	blood vessel

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