Variant report

Variant	rs6749773
Chromosome Location	chr2:48642541-48642542
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:48633890..48635428-chr2:48640629..48643120,2	K562	blood:
2	chr2:48336673..48339163-chr2:48642028..48644836,2	K562	blood:
3	chr2:48641901..48644739-chr2:48646186..48647771,2	K562	blood:

Extended variants
information (count: 135 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:132)

rs_ID	r²[population]
rs10153773	0.82[JPT][hapmap]
rs10169629	0.85[ASN][1000 genomes]
rs10174717	0.83[AMR][1000 genomes]
rs10186237	0.89[CEU][hapmap]
rs10199431	0.89[CEU][hapmap];0.83[JPT][hapmap];0.83[AMR][1000 genomes]
rs10208627	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10211336	0.83[ASN][1000 genomes]
rs10454133	0.85[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10454134	0.83[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs10454143	0.85[ASN][1000 genomes]
rs10495951	0.95[JPT][hapmap]
rs10495952	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs11676168	0.89[CEU][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes]
rs11679523	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs11680719	0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs11680916	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs11682044	0.89[CEU][hapmap]
rs11682931	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11683099	0.84[ASN][1000 genomes]
rs11683639	0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs11683708	0.83[ASN][1000 genomes]
rs11685861	0.96[CEU][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11688481	0.95[JPT][hapmap]
rs11689622	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs11690690	0.96[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11690748	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs11690845	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs12052754	0.80[ASN][1000 genomes]
rs12105983	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12328506	0.86[ASN][1000 genomes]
rs13385535	0.83[AMR][1000 genomes]
rs13388291	0.88[CEU][hapmap];0.81[JPT][hapmap]
rs13392004	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13398791	0.86[ASN][1000 genomes]
rs13399936	0.86[ASN][1000 genomes]
rs13400909	0.86[ASN][1000 genomes]
rs13401749	0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs13401752	0.86[ASN][1000 genomes]
rs13429377	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13432998	0.82[JPT][hapmap];0.80[AMR][1000 genomes]
rs17037289	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs17037298	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs17855177	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs28841370	0.87[AMR][1000 genomes]
rs4267555	0.88[AMR][1000 genomes]
rs4274640	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4316980	0.83[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs4344965	0.96[CEU][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4411759	0.89[CEU][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes]
rs4438532	0.83[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs4494796	0.87[ASN][1000 genomes]
rs4497915	0.83[EUR][1000 genomes]
rs4547570	0.86[ASN][1000 genomes]
rs4547573	0.86[CEU][hapmap]
rs4606978	0.83[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs4641990	0.87[JPT][hapmap]
rs55640438	0.87[ASN][1000 genomes]
rs55660911	0.82[ASN][1000 genomes]
rs55744465	0.90[ASN][1000 genomes]
rs55757090	0.80[ASN][1000 genomes]
rs55971719	0.81[ASN][1000 genomes]
rs56156294	0.90[ASN][1000 genomes]
rs56365822	1.00[ASN][1000 genomes]
rs56391806	0.90[ASN][1000 genomes]
rs57537506	0.81[ASN][1000 genomes]
rs57668696	0.88[AMR][1000 genomes]
rs57893565	0.83[ASN][1000 genomes]
rs58012056	0.83[ASN][1000 genomes]
rs58020097	0.86[ASN][1000 genomes]
rs58969359	0.86[ASN][1000 genomes]
rs58978223	0.99[ASN][1000 genomes]
rs59045263	0.96[ASN][1000 genomes]
rs59761994	0.87[AMR][1000 genomes]
rs60042255	1.00[ASN][1000 genomes]
rs60825643	0.85[ASN][1000 genomes]
rs60988618	0.84[ASN][1000 genomes]
rs61303367	0.99[ASN][1000 genomes]
rs62136987	0.81[AMR][1000 genomes]
rs62137002	0.85[AMR][1000 genomes]
rs62137003	0.85[AMR][1000 genomes]
rs62137015	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62137019	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62137021	0.97[ASN][1000 genomes]
rs62137041	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6545027	0.85[CEU][hapmap]
rs6545030	0.93[CEU][hapmap];0.87[JPT][hapmap];0.88[AMR][1000 genomes]
rs6545034	0.87[AMR][1000 genomes]
rs6545035	0.87[AMR][1000 genomes]
rs6545036	0.96[CEU][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6545039	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs66705539	0.98[ASN][1000 genomes]
rs6705802	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs6712029	0.92[CEU][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes]
rs6718068	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs6722246	0.83[ASN][1000 genomes]
rs6732196	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6735288	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6743757	0.96[CEU][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6745580	0.81[ASN][1000 genomes]
rs6756596	0.86[ASN][1000 genomes]
rs6757206	0.81[AMR][1000 genomes]
rs72820404	0.80[ASN][1000 genomes]
rs72820405	0.87[AMR][1000 genomes]
rs72820420	0.81[ASN][1000 genomes]
rs72820422	0.81[ASN][1000 genomes]
rs72820423	0.83[ASN][1000 genomes]
rs72820424	0.80[ASN][1000 genomes]
rs72820427	0.83[ASN][1000 genomes]
rs72820433	0.82[ASN][1000 genomes]
rs72820436	0.82[ASN][1000 genomes]
rs72820437	0.83[ASN][1000 genomes]
rs72820439	0.83[ASN][1000 genomes]
rs72820441	0.80[ASN][1000 genomes]
rs72820445	0.83[ASN][1000 genomes]
rs72820454	1.00[ASN][1000 genomes]
rs72820474	0.86[ASN][1000 genomes]
rs72820479	0.87[ASN][1000 genomes]
rs72820484	0.86[ASN][1000 genomes]
rs72820492	0.84[ASN][1000 genomes]
rs72820494	0.86[ASN][1000 genomes]
rs72820499	0.85[ASN][1000 genomes]
rs7562069	0.96[CEU][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7562816	0.96[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7565792	0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs7566239	0.96[JPT][hapmap];0.82[ASN][1000 genomes]
rs7568574	0.96[ASN][1000 genomes]
rs7573316	0.83[ASN][1000 genomes]
rs7576964	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs7577237	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs7579932	1.00[CEU][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7600794	0.96[CEU][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7606104	0.96[CEU][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762252	chr2:48554150-48741093	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv581775	chr2:48619869-48714938	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv518718	chr2:48624007-48650308	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6749773	PPP1R21	cis	Thyroid	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48638400-48643400	Weak transcription	Gastric	stomach
2	chr2:48639600-48645200	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr2:48639600-48647400	Enhancers	Liver	Liver
4	chr2:48640000-48643600	Enhancers	Fetal Intestine Large	intestine
5	chr2:48640000-48646200	Enhancers	Fetal Intestine Small	intestine
6	chr2:48640400-48642800	Weak transcription	Fetal Kidney	kidney
7	chr2:48640400-48647600	Weak transcription	Colon Smooth Muscle	Colon
8	chr2:48640400-48647600	Weak transcription	Ovary	ovary
9	chr2:48640600-48647800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:48640800-48643400	Weak transcription	Fetal Stomach	stomach
11	chr2:48641000-48647400	Weak transcription	Stomach Smooth Muscle	stomach
12	chr2:48641400-48642600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr2:48641400-48643600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr2:48641400-48643800	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr2:48641800-48642600	Enhancers	Primary T cells from cord blood	blood
16	chr2:48641800-48643000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:48641800-48643200	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr2:48641800-48643600	Enhancers	Primary hematopoietic stem cells	blood
19	chr2:48641800-48643800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:48641800-48643800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:48641800-48643800	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr2:48641800-48643800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr2:48641800-48643800	Enhancers	Fetal Brain Female	brain
24	chr2:48641800-48643800	Flanking Active TSS	HepG2	liver
25	chr2:48641800-48643800	Enhancers	HSMMtube	muscle
26	chr2:48641800-48644000	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr2:48642000-48642600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr2:48642000-48642800	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr2:48642000-48642800	Flanking Active TSS	Brain Germinal Matrix	brain
30	chr2:48642000-48642800	Enhancers	Osteobl	bone
31	chr2:48642000-48643000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
32	chr2:48642000-48643000	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr2:48642000-48643400	Flanking Active TSS	Brain Hippocampus Middle	brain
34	chr2:48642000-48643600	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr2:48642000-48643600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr2:48642000-48643600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr2:48642000-48643600	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr2:48642000-48643600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr2:48642000-48643600	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr2:48642000-48643600	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr2:48642000-48643600	Enhancers	Rectal Mucosa Donor 29	rectum
42	chr2:48642000-48643600	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr2:48642000-48643600	Enhancers	Dnd41	blood
44	chr2:48642000-48643600	Enhancers	Monocytes-CD14+_RO01746	blood
45	chr2:48642000-48643600	Enhancers	NHDF-Ad	bronchial
46	chr2:48642000-48643800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr2:48642000-48643800	Enhancers	Primary T helper cells fromperipheralblood	blood
48	chr2:48642000-48643800	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr2:48642200-48642600	Active TSS	Brain Angular Gyrus	brain
50	chr2:48642200-48642600	Active TSS	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links