Variant report

Variant	rs2893242
Chromosome Location	chr1:93705532-93705533
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	chr1:93695649..93698246-chr1:93704772..93706327,2	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10874766	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11164885	0.89[ASN][1000 genomes]
rs11164896	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11164905	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12027142	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12030843	0.89[ASN][1000 genomes]
rs12031709	0.80[ASN][1000 genomes]
rs12031765	0.89[ASN][1000 genomes]
rs12033147	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12036057	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12038046	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12044557	0.89[ASN][1000 genomes]
rs12045001	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12046063	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12048219	0.90[ASN][1000 genomes]
rs12405487	0.82[ASN][1000 genomes]
rs12563709	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2255722	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2391251	0.82[ASN][1000 genomes]
rs2484486	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2783490	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2783493	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2783495	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2783496	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2783497	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2783505	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2815406	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28782525	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087457	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3904665	0.89[ASN][1000 genomes]
rs3904666	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4484937	0.87[ASN][1000 genomes]
rs58354545	0.89[ASN][1000 genomes]
rs61799470	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61799497	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61799500	0.89[ASN][1000 genomes]
rs61799516	0.82[ASN][1000 genomes]
rs61799517	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61799538	0.90[ASN][1000 genomes]
rs6676902	0.82[ASN][1000 genomes]
rs6684908	0.82[ASN][1000 genomes]
rs72959220	0.89[ASN][1000 genomes]
rs771454	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs771461	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs771465	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs771476	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs771479	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs771482	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs810027	0.80[EUR][1000 genomes];0.80[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	nsv830625	chr1:93566378-93735246	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2893242	DR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93647000-93756400	Weak transcription	Gastric	stomach
2	chr1:93647200-93707400	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr1:93647200-93757600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr1:93647600-93706600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:93654200-93708400	Weak transcription	Esophagus	oesophagus
6	chr1:93654600-93708000	Weak transcription	Ovary	ovary
7	chr1:93657600-93708400	Weak transcription	Left Ventricle	heart
8	chr1:93661400-93708200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr1:93661800-93708200	Weak transcription	Fetal Brain Female	brain
10	chr1:93663600-93705600	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr1:93665400-93708400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr1:93665400-93708400	Weak transcription	Spleen	Spleen
13	chr1:93665600-93707800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:93665800-93706600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:93665800-93707800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:93666600-93727000	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr1:93668800-93708400	Weak transcription	Duodenum Mucosa	Duodenum
18	chr1:93672600-93708400	Weak transcription	Placenta	Placenta
19	chr1:93673800-93707400	Weak transcription	A549	lung
20	chr1:93682400-93708800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr1:93684800-93708400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:93685200-93707400	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr1:93685400-93708400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr1:93685600-93708400	Weak transcription	NH-A	brain
25	chr1:93685600-93709200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr1:93686600-93706600	Weak transcription	Fetal Muscle Leg	muscle
27	chr1:93686600-93708400	Weak transcription	Aorta	Aorta
28	chr1:93686800-93708400	Weak transcription	Fetal Lung	lung
29	chr1:93687000-93705600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr1:93688000-93705600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr1:93688200-93714800	Weak transcription	HSMMtube	muscle
32	chr1:93689200-93708400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:93690200-93707400	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr1:93690200-93708600	Weak transcription	NHLF	lung
35	chr1:93690400-93729400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr1:93691200-93732400	Weak transcription	HUVEC	blood vessel
37	chr1:93692200-93787800	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr1:93693400-93706600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr1:93693400-93709200	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr1:93694000-93706600	Weak transcription	Thymus	Thymus
41	chr1:93694200-93707800	Weak transcription	Fetal Stomach	stomach
42	chr1:93695200-93705600	Weak transcription	HSMM	muscle
43	chr1:93696800-93706200	Weak transcription	Fetal Brain Male	brain
44	chr1:93697400-93706600	Strong transcription	Fetal Thymus	thymus
45	chr1:93697800-93706000	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr1:93698600-93705800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr1:93698600-93706600	Weak transcription	Fetal Intestine Small	intestine
48	chr1:93700200-93707600	Strong transcription	Primary B cells from cord blood	blood
49	chr1:93700400-93706600	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr1:93701200-93705600	Weak transcription	Primary T cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links