Variant report

Variant	rs1983378
Chromosome Location	chr4:57249092-57249093
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 98 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10008223	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10010544	0.86[EUR][1000 genomes]
rs10013402	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10017460	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10051	0.81[ASN][1000 genomes]
rs10434444	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10434445	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10461357	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1060472	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11133442	0.83[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11133443	1.00[CEU][hapmap]
rs1124569	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11723782	0.86[EUR][1000 genomes]
rs12498340	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12501334	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12501502	0.90[YRI][hapmap]
rs12503412	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12504291	0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes]
rs12505939	0.81[ASN][1000 genomes]
rs12508008	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs12509542	0.83[ASN][1000 genomes]
rs12510712	0.84[ASN][1000 genomes]
rs12511770	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12512742	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12513091	0.83[ASN][1000 genomes]
rs12646890	0.83[ASN][1000 genomes]
rs13147900	0.95[JPT][hapmap]
rs1401904	0.95[JPT][hapmap]
rs1401906	0.95[JPT][hapmap];0.80[YRI][hapmap]
rs14211	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs1474179	0.91[ASN][1000 genomes]
rs1520030	0.91[YRI][hapmap];0.80[AFR][1000 genomes]
rs17086696	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17086794	0.88[ASN][1000 genomes]
rs17086832	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs17086853	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs1967559	0.83[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2030366	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2049088	0.85[EUR][1000 genomes]
rs2271923	0.90[YRI][hapmap]
rs2271925	0.89[EUR][1000 genomes]
rs28510634	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28866881	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3796548	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs3822001	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs4263445	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4340842	0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs4346704	0.86[ASN][1000 genomes]
rs4493603	0.90[YRI][hapmap]
rs4618376	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs4864579	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4864580	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4864583	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4865088	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4865089	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4865092	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4865103	0.85[ASN][1000 genomes]
rs4865107	0.83[ASN][1000 genomes]
rs4865108	0.81[ASN][1000 genomes]
rs5010012	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs55915354	0.81[ASN][1000 genomes]
rs56040009	0.81[ASN][1000 genomes]
rs56066795	0.89[EUR][1000 genomes]
rs56099714	0.83[ASN][1000 genomes]
rs56356367	0.84[EUR][1000 genomes]
rs56392224	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs56887793	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58151706	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs59997251	0.83[EUR][1000 genomes]
rs60104031	0.82[EUR][1000 genomes]
rs61032900	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6554344	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs6554345	0.95[JPT][hapmap]
rs6554358	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs66858948	0.88[ASN][1000 genomes]
rs66863699	0.83[ASN][1000 genomes]
rs67957495	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6820279	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6820314	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6821301	0.92[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6824893	0.80[ASN][1000 genomes]
rs6829250	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6832797	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6834696	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6834736	0.95[JPT][hapmap]
rs6836118	1.00[CEU][hapmap]
rs6846895	0.80[AFR][1000 genomes]
rs6849183	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs6855041	0.81[YRI][hapmap]
rs7664841	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7670991	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7696808	1.00[CEU][hapmap];0.85[YRI][hapmap];0.89[EUR][1000 genomes]
rs8340	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]

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	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv829940	chr4:57072341-57262730	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
5	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1983378	SRP72	cis	normal skin	skin_eQTL
rs1983378	SRP72	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57190600-57252400	Weak transcription	Colonic Mucosa	Colon
2	chr4:57202800-57252400	Weak transcription	NHDF-Ad	bronchial
3	chr4:57203000-57252600	Weak transcription	Right Ventricle	heart
4	chr4:57203200-57251800	Weak transcription	A549	lung
5	chr4:57203400-57252400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr4:57204000-57252200	Weak transcription	NH-A	brain
7	chr4:57204200-57252200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr4:57204800-57251800	Weak transcription	Fetal Brain Male	brain
9	chr4:57207800-57253000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr4:57211000-57251600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr4:57211800-57252200	Weak transcription	Fetal Heart	heart
12	chr4:57212400-57251800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr4:57213400-57251600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr4:57213400-57252200	Weak transcription	NHLF	lung
15	chr4:57213600-57250200	Weak transcription	K562	blood
16	chr4:57213600-57252000	Weak transcription	HMEC	breast
17	chr4:57214400-57251800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr4:57214600-57252200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr4:57215800-57251600	Weak transcription	Brain Anterior Caudate	brain
20	chr4:57216000-57251800	Weak transcription	HepG2	liver
21	chr4:57216000-57252400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr4:57216000-57253000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr4:57216400-57251800	Weak transcription	Psoas Muscle	Psoas
24	chr4:57223000-57253200	Weak transcription	Esophagus	oesophagus
25	chr4:57223200-57253200	Weak transcription	Gastric	stomach
26	chr4:57223600-57251600	Weak transcription	Fetal Kidney	kidney
27	chr4:57225000-57252200	Weak transcription	Duodenum Mucosa	Duodenum
28	chr4:57227400-57252400	Weak transcription	NHEK	skin
29	chr4:57229800-57251800	Weak transcription	Thymus	Thymus
30	chr4:57229800-57252400	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr4:57229800-57252400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr4:57229800-57252400	Weak transcription	Brain Germinal Matrix	brain
33	chr4:57229800-57253000	Weak transcription	Ovary	ovary
34	chr4:57229800-57253200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr4:57229800-57253200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr4:57232800-57252400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr4:57232800-57252400	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr4:57232800-57253000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr4:57235600-57252400	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr4:57236400-57251800	Weak transcription	Brain Angular Gyrus	brain
41	chr4:57236400-57252200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr4:57236600-57252400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr4:57236600-57253000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr4:57236600-57253200	Weak transcription	Lung	lung
45	chr4:57236800-57253000	Weak transcription	Aorta	Aorta
46	chr4:57236800-57253000	Weak transcription	Left Ventricle	heart
47	chr4:57237000-57252400	Weak transcription	Osteobl	bone
48	chr4:57237000-57252600	Weak transcription	Fetal Stomach	stomach
49	chr4:57237200-57251800	Weak transcription	Fetal Brain Female	brain
50	chr4:57237200-57252400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links