Variant report

Variant	rs2952144
Chromosome Location	chr17:37960017-37960018
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:37959637..37962803-chr17:37963434..37965608,3	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10445308	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11658993	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12942330	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12944882	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12946510	0.88[ASN][1000 genomes]
rs2313430	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2941522	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2952140	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3816470	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4795395	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs907091	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs907092	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9303277	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9747973	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9909593	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9916765	0.81[EUR][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	nsv1064787	chr17:37892843-38054410	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv543342	chr17:37892843-38054410	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2952144	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL
rs2952144	GSDML	Cis_1M	lymphoblastoid	RTeQTL
rs2952144	GSDMB	cis	Whole Blood	GTEx
rs2952144	GSDMA	cis	Adipose Subcutaneous	GTEx
rs2952144	ORMDL3	cis	Whole Blood	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37939000-37961800	Weak transcription	Spleen	Spleen
2	chr17:37951600-37969800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr17:37957200-37961000	Weak transcription	Duodenum Mucosa	Duodenum
4	chr17:37957800-37961000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr17:37957800-37961200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr17:37957800-37968800	Weak transcription	Thymus	Thymus
7	chr17:37958200-37961000	Weak transcription	GM12878-XiMat	blood
8	chr17:37958800-37961200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr17:37958800-37968600	Weak transcription	Fetal Thymus	thymus
10	chr17:37959000-37960800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr17:37959400-37960200	Weak transcription	Primary T cells from cord blood	blood
12	chr17:37959400-37960200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr17:37959400-37960400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr17:37959400-37960800	Strong transcription	Primary B cells from peripheral blood	blood
15	chr17:37959400-37960800	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr17:37959400-37961000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr17:37959400-37961200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr17:37959400-37961200	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr17:37959400-37962800	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr17:37959400-37967200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr17:37959400-37968200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr17:37959600-37961000	Strong transcription	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links