Variant report

Variant	rs11556200
Chromosome Location	chr1:45444038-45444039
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45245416..45248456-chr1:45442657..45444544,3	K562	blood:
2	chr1:45443941..45446548-chr1:45450111..45452073,2	K562	blood:
3	chr1:45282334..45285552-chr1:45442428..45444971,3	K562	blood:
4	chr1:45186345..45187927-chr1:45443599..45445522,2	K562	blood:
5	chr1:45273709..45275495-chr1:45442746..45445462,2	K562	blood:

Variant related genes	Relation type
ENSG00000234093	Chromatin interaction
ENSG00000222009	Chromatin interaction
ENSG00000199377	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10890316	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10890317	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10890318	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11211036	0.84[JPT][hapmap]
rs11211038	0.85[CHD][hapmap];0.83[JPT][hapmap]
rs11211040	0.85[CHD][hapmap];0.84[JPT][hapmap]
rs11211053	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs11211059	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11211060	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211066	0.84[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.82[EUR][1000 genomes]
rs11211067	0.84[CEU][hapmap]
rs11573562	0.89[CHD][hapmap]
rs11576875	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11584440	0.85[CHD][hapmap]
rs11586398	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11588468	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11802780	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11806079	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11809982	0.84[CEU][hapmap];0.84[CHB][hapmap];0.80[EUR][1000 genomes]
rs11811656	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12070692	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12082902	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12117191	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12117432	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12122911	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12122946	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12125188	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12126314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12126318	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12127012	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12127100	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12127262	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12133015	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12134146	0.82[AFR][1000 genomes]
rs12139143	0.84[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap]
rs12142881	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12144152	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1226360	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1226361	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12724852	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12725055	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12731245	0.84[CEU][hapmap];0.89[CHB][hapmap]
rs12732402	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12733586	0.89[JPT][hapmap]
rs12735637	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12738406	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12738542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12738586	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12740561	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12742371	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12749130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12749939	0.84[CEU][hapmap];0.84[CHB][hapmap]
rs12750107	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12755554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12758547	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13948	0.84[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap]
rs17393404	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17881698	0.85[CHD][hapmap]
rs17883049	0.82[CHD][hapmap];0.84[JPT][hapmap]
rs183809	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2133503	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2236576	0.84[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap]
rs2275598	0.82[AFR][1000 genomes]
rs2275599	0.82[AFR][1000 genomes]
rs2295997	0.82[CHD][hapmap];0.82[JPT][hapmap]
rs2487367	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs263988	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs263989	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs263991	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.82[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs263992	1.00[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.82[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs263994	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs263996	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs263997	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs264020	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs264021	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs264022	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs264023	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs264024	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs264025	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28409260	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs364482	0.90[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];0.83[YRI][hapmap];0.94[ASN][1000 genomes]
rs3795719	0.84[JPT][hapmap]
rs3806405	0.84[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes]
rs4399199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs544144	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs566063	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56875328	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6429550	0.89[JPT][hapmap]
rs656780	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6659033	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6659777	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6676749	0.85[CHD][hapmap]
rs6678726	0.84[CEU][hapmap];0.84[CHB][hapmap];0.85[CHD][hapmap]
rs6678762	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6678769	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6692487	0.89[JPT][hapmap]
rs6692713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6703452	0.84[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap]
rs67863058	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs68175913	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7517439	0.96[CHD][hapmap];0.89[JPT][hapmap]
rs7517639	0.89[JPT][hapmap]
rs7519454	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7521339	0.81[EUR][1000 genomes]
rs7525733	0.84[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.83[EUR][1000 genomes]
rs7535347	0.84[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7541207	0.84[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap]
rs7541351	0.84[CEU][hapmap];0.84[CHB][hapmap]
rs7553658	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8681	0.84[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes]
rs998418	0.84[CEU][hapmap];0.89[CHD][hapmap];0.82[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
2	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
3	nsv915644	chr1:45282802-45696079	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
5	esv2830314	chr1:45430218-45455285	Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs11556200	NASP	cis	cerebellum	SCAN
rs11556200	SNORD38A	cis	cerebellum	SCAN
rs11556200	SNORD55	cis	parietal	SCAN
rs11556200	ZNF691	cis	cerebellum	SCAN
rs11556200	EIF2B3	cis	parietal	SCAN
rs11556200	SNORD55	cis	cerebellum	SCAN
rs11556200	UROD	cis	Artery Tibial	GTEx
rs11556200	UROD	cis	Adipose Subcutaneous	GTEx
rs11556200	EIF2B3	cis	cerebellum	SCAN
rs11556200	UROD	cis	Esophagus Muscularis	GTEx
rs11556200	UROD	cis	multi-tissue	Pritchard

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45389200-45450200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr1:45414000-45450800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr1:45414000-45451000	Weak transcription	Spleen	Spleen
4	chr1:45421000-45450800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:45424800-45445600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:45425000-45445600	Weak transcription	Aorta	Aorta
7	chr1:45430800-45450800	Weak transcription	Brain Substantia Nigra	brain
8	chr1:45433200-45451000	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr1:45434400-45450800	Weak transcription	Small Intestine	intestine
10	chr1:45435600-45444200	Strong transcription	Primary T cells from cord blood	blood
11	chr1:45435600-45447400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:45435600-45447600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:45436000-45447000	Strong transcription	Fetal Muscle Leg	muscle
14	chr1:45436200-45446800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr1:45436400-45450800	Weak transcription	HMEC	breast
16	chr1:45436600-45450800	Weak transcription	Stomach Mucosa	stomach
17	chr1:45436800-45445000	Weak transcription	Hela-S3	cervix
18	chr1:45437200-45444200	Strong transcription	Skeletal Muscle Female	skeletal muscle
19	chr1:45437200-45446800	Strong transcription	Fetal Thymus	thymus
20	chr1:45437400-45444800	Weak transcription	HUVEC	blood vessel
21	chr1:45437400-45446600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:45437400-45447400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr1:45437600-45446800	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr1:45437600-45447000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:45437600-45447200	Strong transcription	Fetal Muscle Trunk	muscle
26	chr1:45437800-45446800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:45438000-45451000	Weak transcription	A549	lung
28	chr1:45438200-45446800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr1:45438200-45447200	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr1:45438200-45450800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr1:45438400-45444200	Strong transcription	Muscle Satellite Cultured Cells	--
32	chr1:45438400-45446800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr1:45438400-45446800	Strong transcription	Duodenum Mucosa	Duodenum
34	chr1:45438400-45447000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:45438400-45447200	Strong transcription	Dnd41	blood
36	chr1:45438400-45451000	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr1:45438600-45444200	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr1:45438600-45447200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr1:45438600-45450800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr1:45439400-45445200	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr1:45439600-45446800	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr1:45439600-45447200	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr1:45439800-45445400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:45439800-45445400	Strong transcription	Fetal Intestine Large	intestine
45	chr1:45439800-45447000	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr1:45440000-45445800	Strong transcription	Fetal Lung	lung
47	chr1:45440000-45446800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr1:45440000-45446800	Strong transcription	Brain Angular Gyrus	brain
49	chr1:45440200-45444200	Strong transcription	NHDF-Ad	bronchial
50	chr1:45440400-45445200	Strong transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links