Variant report

Variant	rs256567
Chromosome Location	chr2:190727531-190727532
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs1030136	0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs11688123	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12479375	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs12618262	0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs12997257	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16832155	0.80[ASN][1000 genomes]
rs16832158	0.84[ASN][1000 genomes]
rs256539	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs256540	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs256541	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs256542	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs256549	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs256550	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs256551	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs256552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs256556	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs256562	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs256563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs256564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs256572	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs256580	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4920654	0.84[ASN][1000 genomes]
rs4920660	0.82[ASN][1000 genomes]
rs4920662	0.82[ASN][1000 genomes]
rs5743112	0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs5743116	0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs5743117	0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs5743202	0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs5743208	0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs6736360	0.85[JPT][hapmap]
rs733318	0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs7593661	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7603201	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[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	nsv213327	chr2:190726489-190729383	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS	lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs256567	LOC51240	cis	multi-tissue	Pritchard
rs256567	ASNSD1	cis	Esophagus Muscularis	GTEx
rs256567	ORMDL1	Cis_1M	lymphoblastoid	RTeQTL
rs256567	PMS1	Cis_1M	lymphoblastoid	RTeQTL
rs256567	ASNSD1	cis	Whole Blood	GTEx
rs256567	TNFSF10	trans	lymphoblastoid	RTeQTL
rs256567	ORMDL1	cis	Lymphoblastoid	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190658200-190743800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr2:190659800-190743600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:190664800-190741800	Weak transcription	Brain Angular Gyrus	brain
4	chr2:190669400-190743800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr2:190681000-190743000	Weak transcription	Brain Germinal Matrix	brain
6	chr2:190684000-190743600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr2:190685000-190736400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:190685400-190739400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr2:190685400-190741800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:190687000-190738400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:190687000-190738400	Weak transcription	Lung	lung
12	chr2:190691000-190744200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr2:190701200-190743200	Weak transcription	Fetal Brain Male	brain
14	chr2:190701400-190744000	Weak transcription	Fetal Brain Female	brain
15	chr2:190701600-190743200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr2:190701600-190744800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr2:190701800-190745200	Weak transcription	Fetal Kidney	kidney
18	chr2:190702400-190745600	Weak transcription	Colon Smooth Muscle	Colon
19	chr2:190705200-190740000	Weak transcription	Right Ventricle	heart
20	chr2:190706800-190742800	Weak transcription	Fetal Heart	heart
21	chr2:190707000-190738200	Weak transcription	Brain Hippocampus Middle	brain
22	chr2:190707000-190741400	Weak transcription	Brain Anterior Caudate	brain
23	chr2:190707400-190741200	Weak transcription	Brain Substantia Nigra	brain
24	chr2:190707600-190746000	Weak transcription	Left Ventricle	heart
25	chr2:190708400-190743400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr2:190708800-190744400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr2:190709600-190744000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr2:190710600-190741800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr2:190711800-190733000	Weak transcription	Spleen	Spleen
30	chr2:190713200-190743400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr2:190713200-190743800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr2:190713200-190745600	Weak transcription	Pancreas	Pancrea
33	chr2:190713800-190727600	Weak transcription	Fetal Muscle Trunk	muscle
34	chr2:190713800-190729600	Weak transcription	Fetal Lung	lung
35	chr2:190713800-190743800	Weak transcription	Fetal Intestine Large	intestine
36	chr2:190713800-190744400	Weak transcription	Gastric	stomach
37	chr2:190713800-190744800	Weak transcription	K562	blood
38	chr2:190714000-190728400	Weak transcription	Fetal Thymus	thymus
39	chr2:190714600-190743800	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr2:190714600-190744000	Weak transcription	Fetal Stomach	stomach
41	chr2:190714600-190744400	Weak transcription	Psoas Muscle	Psoas
42	chr2:190714800-190728800	Weak transcription	Adipose Nuclei	Adipose
43	chr2:190714800-190745200	Weak transcription	NHEK	skin
44	chr2:190715000-190741800	Weak transcription	Aorta	Aorta
45	chr2:190715200-190730600	Weak transcription	Placenta	Placenta
46	chr2:190715600-190744800	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr2:190716000-190743400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr2:190716600-190743400	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr2:190716600-190744200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr2:190716800-190744200	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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