Variant report

Variant	rs17271246
Chromosome Location	chr2:190646207-190646208
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:190639387..190641979-chr2:190643481..190646316,2	K562	blood:
2	chr2:190626354..190628880-chr2:190644961..190646974,2	K562	blood:
3	chr2:190524324..190528374-chr2:190645867..190651485,5	K562	blood:
4	chr2:190639477..190641367-chr2:190643907..190646225,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138381	Chromatin interaction
ENSG00000128694	Chromatin interaction
ENSG00000253559	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs1233255	0.82[JPT][hapmap]
rs1233276	0.82[JPT][hapmap]
rs16831704	1.00[CHB][hapmap]
rs16831706	1.00[CHB][hapmap]
rs16831726	1.00[CHB][hapmap]
rs16831821	0.80[EUR][1000 genomes]
rs16831873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16831944	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16831972	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2164830	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2278591	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2289405	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56137655	0.86[EUR][1000 genomes]
rs56324258	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5742926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5742985	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5743047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5743072	1.00[JPT][hapmap]
rs5743077	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62183651	0.82[EUR][1000 genomes]
rs62183652	0.82[EUR][1000 genomes]
rs62183653	0.82[EUR][1000 genomes]
rs62183656	0.86[EUR][1000 genomes]
rs62183658	0.85[EUR][1000 genomes]
rs62183659	0.86[EUR][1000 genomes]
rs62184265	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62184267	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62184268	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62184285	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs62185869	0.86[EUR][1000 genomes]
rs62185872	0.88[EUR][1000 genomes]
rs62185874	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62185897	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6434372	1.00[CHB][hapmap]
rs6748102	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6753164	1.00[JPT][hapmap]
rs72920421	0.82[EUR][1000 genomes]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17271246	ORMDL1	cis	Skin Sun Exposed Lower leg	GTEx
rs17271246	ORMDL1	cis	multi-tissue	Pritchard
rs17271246	ORMDL1	Cis_1M	lymphoblastoid	RTeQTL
rs17271246	PMS1	Cis_1M	lymphoblastoid	RTeQTL
rs17271246	ORMDL1	cis	normal skin	skin_eQTL
rs17271246	ORMDL1	cis	Muscle Skeletal	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190627800-190648200	Weak transcription	Gastric	stomach
2	chr2:190628200-190648000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:190628200-190648000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:190628200-190648200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:190628400-190648000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr2:190628600-190647000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr2:190628600-190647200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr2:190628600-190647200	Weak transcription	Stomach Mucosa	stomach
9	chr2:190628600-190648400	Weak transcription	Small Intestine	intestine
10	chr2:190629000-190647200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:190629800-190647000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:190630000-190646600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr2:190630800-190647000	Strong transcription	HSMM	muscle
14	chr2:190631200-190647200	Strong transcription	Fetal Thymus	thymus
15	chr2:190631400-190646800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr2:190631600-190647000	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr2:190632000-190646600	Strong transcription	Placenta	Placenta
18	chr2:190632800-190647200	Strong transcription	Primary B cells from peripheral blood	blood
19	chr2:190633200-190646800	Strong transcription	HMEC	breast
20	chr2:190633600-190646600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr2:190634000-190646400	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr2:190634000-190647000	Strong transcription	Osteobl	bone
23	chr2:190634200-190647400	Strong transcription	Fetal Muscle Trunk	muscle
24	chr2:190634600-190646400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr2:190634600-190646600	Strong transcription	Muscle Satellite Cultured Cells	--
26	chr2:190634600-190647000	Strong transcription	NH-A	brain
27	chr2:190634600-190647200	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr2:190634600-190647200	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr2:190634600-190647200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr2:190635000-190647000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr2:190635000-190647200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr2:190635200-190646400	Strong transcription	Duodenum Mucosa	Duodenum
33	chr2:190635200-190647200	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr2:190636200-190646800	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr2:190636400-190647000	Weak transcription	Aorta	Aorta
36	chr2:190637000-190646400	Strong transcription	Fetal Lung	lung
37	chr2:190638200-190647000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr2:190640200-190647200	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr2:190641200-190647000	Weak transcription	Rectal Smooth Muscle	rectum
40	chr2:190641600-190647200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr2:190641800-190648000	Weak transcription	Colonic Mucosa	Colon
42	chr2:190642200-190647000	Weak transcription	K562	blood
43	chr2:190642600-190647000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr2:190642800-190647000	Weak transcription	Hela-S3	cervix
45	chr2:190643200-190647200	Strong transcription	Fetal Muscle Leg	muscle
46	chr2:190643600-190647600	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr2:190643800-190647000	Strong transcription	A549	lung
48	chr2:190644000-190646400	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr2:190644000-190646800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr2:190644000-190647000	Genic enhancers	Primary T helper cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links