Variant report

Variant	rs2503849
Chromosome Location	chr10:43672776-43672777
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 109 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1059484	1.00[ASN][1000 genomes]
rs10793422	0.96[ASN][1000 genomes]
rs10793424	0.92[ASN][1000 genomes]
rs10793426	0.91[ASN][1000 genomes]
rs10793427	0.91[ASN][1000 genomes]
rs10899778	0.91[ASN][1000 genomes]
rs10899779	0.92[ASN][1000 genomes]
rs10899780	0.91[ASN][1000 genomes]
rs10899781	0.90[ASN][1000 genomes]
rs10899782	0.92[ASN][1000 genomes]
rs10899786	0.91[ASN][1000 genomes]
rs10899787	0.87[ASN][1000 genomes]
rs11238476	0.92[ASN][1000 genomes]
rs11238479	0.92[ASN][1000 genomes]
rs11238481	0.91[ASN][1000 genomes]
rs11238483	0.90[ASN][1000 genomes]
rs11238485	0.90[ASN][1000 genomes]
rs11238490	0.91[ASN][1000 genomes]
rs11528481	0.92[ASN][1000 genomes]
rs12220534	0.92[ASN][1000 genomes]
rs12241923	0.84[EUR][1000 genomes]
rs12268309	0.91[ASN][1000 genomes]
rs12356643	0.87[ASN][1000 genomes]
rs12360493	0.91[ASN][1000 genomes]
rs12416428	0.90[ASN][1000 genomes]
rs1254958	0.98[ASN][1000 genomes]
rs1254959	0.99[ASN][1000 genomes]
rs1254960	1.00[ASN][1000 genomes]
rs1254962	1.00[ASN][1000 genomes]
rs1254963	1.00[ASN][1000 genomes]
rs1254965	1.00[ASN][1000 genomes]
rs1254967	1.00[ASN][1000 genomes]
rs1254968	1.00[ASN][1000 genomes]
rs1270015	1.00[ASN][1000 genomes]
rs1272142	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1317214	0.88[ASN][1000 genomes]
rs17153156	0.90[EUR][1000 genomes]
rs1800861	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1864395	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1864399	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1864400	0.86[ASN][1000 genomes]
rs1879310	0.92[ASN][1000 genomes]
rs1915142	0.90[ASN][1000 genomes]
rs2003317	1.00[ASN][1000 genomes]
rs2075910	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2075912	0.88[ASN][1000 genomes]
rs2075913	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2115817	1.00[ASN][1000 genomes]
rs2249005	0.91[ASN][1000 genomes]
rs2257767	0.99[ASN][1000 genomes]
rs2293020	1.00[ASN][1000 genomes]
rs2435337	0.99[ASN][1000 genomes]
rs2435338	0.94[ASN][1000 genomes]
rs2435339	0.94[ASN][1000 genomes]
rs2435354	0.99[ASN][1000 genomes]
rs2435376	0.97[ASN][1000 genomes]
rs2435377	1.00[ASN][1000 genomes]
rs2435383	1.00[ASN][1000 genomes]
rs2435384	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2435385	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2503841	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2503848	1.00[ASN][1000 genomes]
rs2503853	0.83[ASN][1000 genomes]
rs2503860	1.00[ASN][1000 genomes]
rs2503863	1.00[ASN][1000 genomes]
rs2503864	1.00[ASN][1000 genomes]
rs2503865	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2503866	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2503881	1.00[ASN][1000 genomes]
rs2505505	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2505506	0.97[ASN][1000 genomes]
rs2505511	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2505512	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2505513	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2505514	0.91[ASN][1000 genomes]
rs2505553	1.00[ASN][1000 genomes]
rs2505554	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2505557	0.99[ASN][1000 genomes]
rs2565200	0.88[ASN][1000 genomes]
rs2565201	0.88[ASN][1000 genomes]
rs2742233	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2742234	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2742235	0.83[ASN][1000 genomes]
rs2742237	0.88[ASN][1000 genomes]
rs2742239	0.88[ASN][1000 genomes]
rs2742240	0.91[ASN][1000 genomes]
rs2742241	0.91[ASN][1000 genomes]
rs3004211	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3004214	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4648313	0.92[ASN][1000 genomes]
rs60845448	0.92[ASN][1000 genomes]
rs61268333	0.92[ASN][1000 genomes]
rs61845684	0.91[ASN][1000 genomes]
rs7073849	0.92[ASN][1000 genomes]
rs7093409	0.92[ASN][1000 genomes]
rs7096500	0.94[ASN][1000 genomes]
rs7098236	0.92[ASN][1000 genomes]
rs7098237	0.92[ASN][1000 genomes]
rs715106	0.87[ASN][1000 genomes]
rs741968	0.86[ASN][1000 genomes]
rs871763	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534548	chr10:42890664-43729688	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv430159	chr10:43291894-43946294	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv895082	chr10:43530071-43755506	Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv895083	chr10:43549708-43765485	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv916378	chr10:43622151-43868356	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv1042310	chr10:43623060-43688505	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv1043661	chr10:43626619-43890162	Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv540574	chr10:43626619-43890162	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2503849	CSGALNACT2	cis	Skin Sun Exposed Lower leg	GTEx
rs2503849	CSGALNACT2	cis	Nerve Tibial	GTEx
rs2503849	CSGALNACT2	cis	Heart Left Ventricle	GTEx
rs2503849	CSGALNACT2	cis	Esophagus Muscularis	GTEx
rs2503849	CSGALNACT2	cis	Thyroid	GTEx
rs2503849	CSGALNACT2	cis	Artery Tibial	GTEx
rs2503849	CSGALNACT2	cis	Esophagus Mucosa	GTEx
rs2503849	CSGALNACT2	cis	lung	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43635600-43689000	Weak transcription	Esophagus	oesophagus
2	chr10:43652600-43697200	Weak transcription	Pancreas	Pancrea
3	chr10:43654600-43678000	Weak transcription	Hela-S3	cervix
4	chr10:43655000-43680600	Weak transcription	Colonic Mucosa	Colon
5	chr10:43655800-43673000	Weak transcription	Fetal Kidney	kidney
6	chr10:43656000-43674800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr10:43656400-43673400	Weak transcription	Psoas Muscle	Psoas
8	chr10:43658800-43690600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr10:43659800-43674800	Weak transcription	A549	lung
10	chr10:43660000-43673000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr10:43660400-43687400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr10:43662000-43677000	Strong transcription	Osteobl	bone
13	chr10:43662200-43684400	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr10:43662200-43697600	Weak transcription	NHEK	skin
15	chr10:43662600-43690000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr10:43662800-43681600	Weak transcription	HMEC	breast
17	chr10:43663000-43678000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr10:43663600-43679800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr10:43663600-43683800	Strong transcription	Fetal Thymus	thymus
20	chr10:43663800-43673000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr10:43663800-43673200	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr10:43664000-43673000	Strong transcription	Primary T cells from cord blood	blood
23	chr10:43664000-43673200	Strong transcription	Primary hematopoietic stem cells	blood
24	chr10:43664000-43679600	Strong transcription	Fetal Muscle Trunk	muscle
25	chr10:43664000-43680400	Strong transcription	Dnd41	blood
26	chr10:43664200-43673200	Strong transcription	Primary B cells from peripheral blood	blood
27	chr10:43664200-43676800	Strong transcription	HSMMtube	muscle
28	chr10:43664400-43675600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr10:43664600-43674800	Weak transcription	Lung	lung
30	chr10:43664800-43675000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr10:43665200-43680000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr10:43665400-43679400	Strong transcription	Thymus	Thymus
33	chr10:43665400-43679800	Strong transcription	Adipose Nuclei	Adipose
34	chr10:43665600-43673200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr10:43665600-43673400	Strong transcription	Fetal Muscle Leg	muscle
36	chr10:43665800-43672800	Strong transcription	Fetal Stomach	stomach
37	chr10:43666600-43673200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr10:43666800-43672800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr10:43667400-43679400	Strong transcription	Stomach Smooth Muscle	stomach
40	chr10:43667600-43673200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr10:43667600-43675000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr10:43667600-43679200	Strong transcription	Muscle Satellite Cultured Cells	--
43	chr10:43667800-43685200	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr10:43667800-43692800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr10:43668000-43685200	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr10:43668200-43673200	Weak transcription	Fetal Intestine Small	intestine
47	chr10:43668200-43694000	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr10:43668600-43675000	Weak transcription	Brain Substantia Nigra	brain
49	chr10:43668600-43683800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr10:43668600-43683800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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