Variant report

Variant	rs256572
Chromosome Location	chr2:190717867-190717868
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	chr2:190717819-190717873	ProgFib	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:190713621..190715990-chr2:190716646..190719108,2	MCF-7	breast:

Variant related genes	Relation type
PMS1	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1030136	0.85[ASN][1000 genomes]
rs11688123	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12618262	0.82[ASN][1000 genomes]
rs12997257	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16832155	0.82[ASN][1000 genomes]
rs16832158	0.82[ASN][1000 genomes]
rs256539	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs256540	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs256541	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs256542	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs256549	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs256550	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs256551	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs256552	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs256556	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs256562	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs256563	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs256564	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs256567	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs256580	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4853634	0.81[ASN][1000 genomes]
rs4920654	0.82[ASN][1000 genomes]
rs4920660	0.84[ASN][1000 genomes]
rs4920662	0.80[ASN][1000 genomes]
rs5743112	0.87[ASN][1000 genomes]
rs5743116	0.84[ASN][1000 genomes]
rs5743117	0.84[ASN][1000 genomes]
rs5743202	0.83[ASN][1000 genomes]
rs5743208	0.83[ASN][1000 genomes]
rs6736360	0.80[ASN][1000 genomes]
rs733318	0.87[ASN][1000 genomes]
rs7593661	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7603201	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875617	chr2:190701869-190724141	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs256572	ORMDL1	Cis_1M	lymphoblastoid	RTeQTL
rs256572	PMS1	Cis_1M	lymphoblastoid	RTeQTL
rs256572	TNFSF10	trans	lymphoblastoid	RTeQTL
rs256572	ASNSD1	cis	Whole Blood	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190656800-190721000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr2:190658200-190743800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr2:190659800-190743600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr2:190662800-190719000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr2:190664800-190741800	Weak transcription	Brain Angular Gyrus	brain
6	chr2:190669400-190743800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr2:190671000-190719600	Weak transcription	NH-A	brain
8	chr2:190681000-190743000	Weak transcription	Brain Germinal Matrix	brain
9	chr2:190684000-190743600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr2:190685000-190736400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:190685400-190739400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr2:190685400-190741800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr2:190687000-190724400	Weak transcription	Esophagus	oesophagus
14	chr2:190687000-190738400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:190687000-190738400	Weak transcription	Lung	lung
16	chr2:190691000-190744200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr2:190691400-190719000	Weak transcription	HUVEC	blood vessel
18	chr2:190701200-190743200	Weak transcription	Fetal Brain Male	brain
19	chr2:190701400-190744000	Weak transcription	Fetal Brain Female	brain
20	chr2:190701600-190727400	Weak transcription	HSMMtube	muscle
21	chr2:190701600-190743200	Weak transcription	Stomach Smooth Muscle	stomach
22	chr2:190701600-190744800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr2:190701800-190745200	Weak transcription	Fetal Kidney	kidney
24	chr2:190702400-190745600	Weak transcription	Colon Smooth Muscle	Colon
25	chr2:190703600-190719600	Weak transcription	NHLF	lung
26	chr2:190705200-190740000	Weak transcription	Right Ventricle	heart
27	chr2:190705400-190721400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr2:190706800-190742800	Weak transcription	Fetal Heart	heart
29	chr2:190707000-190738200	Weak transcription	Brain Hippocampus Middle	brain
30	chr2:190707000-190741400	Weak transcription	Brain Anterior Caudate	brain
31	chr2:190707400-190741200	Weak transcription	Brain Substantia Nigra	brain
32	chr2:190707600-190746000	Weak transcription	Left Ventricle	heart
33	chr2:190708400-190743400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr2:190708800-190744400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr2:190709200-190719200	Weak transcription	Osteobl	bone
36	chr2:190709200-190727200	Weak transcription	A549	lung
37	chr2:190709600-190744000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr2:190710600-190741800	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr2:190710800-190719000	Weak transcription	HMEC	breast
40	chr2:190711000-190726800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr2:190711800-190733000	Weak transcription	Spleen	Spleen
42	chr2:190713000-190719400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr2:190713200-190743400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr2:190713200-190743800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr2:190713200-190745600	Weak transcription	Pancreas	Pancrea
46	chr2:190713600-190720600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr2:190713800-190718600	Weak transcription	NHDF-Ad	bronchial
48	chr2:190713800-190718800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr2:190713800-190721200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:190713800-190726400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links