Variant report

Variant	rs4653933
Chromosome Location	chr1:228445187-228445188
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 133 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs1059778	0.82[EUR][1000 genomes]
rs10753445	0.83[EUR][1000 genomes]
rs10799471	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10916271	0.82[EUR][1000 genomes]
rs11578798	0.91[ASN][1000 genomes]
rs11580411	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11581167	0.91[ASN][1000 genomes]
rs11582927	0.91[ASN][1000 genomes]
rs11584385	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11799681	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11804508	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12024649	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12118872	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12726781	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12745416	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1331303	0.95[EUR][1000 genomes]
rs1411910	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1411911	0.86[EUR][1000 genomes]
rs1411913	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1620111	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1629290	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1629294	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1757129	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1757132	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1757133	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1757138	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1757139	0.95[EUR][1000 genomes]
rs1757140	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1757141	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1757142	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1757144	0.95[EUR][1000 genomes]
rs1757145	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1757147	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1757148	0.95[EUR][1000 genomes]
rs1757149	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1757150	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1757151	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1757152	0.93[EUR][1000 genomes]
rs1757155	0.94[EUR][1000 genomes]
rs1757156	0.94[EUR][1000 genomes]
rs1757158	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17640616	0.85[EUR][1000 genomes]
rs1771459	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1771460	0.94[EUR][1000 genomes]
rs1771461	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1771462	0.96[EUR][1000 genomes]
rs1771467	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1771468	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1771469	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1771470	0.94[EUR][1000 genomes]
rs1771471	0.95[EUR][1000 genomes]
rs1771472	0.94[EUR][1000 genomes]
rs1771474	0.95[EUR][1000 genomes]
rs1771476	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1771477	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1771478	0.94[EUR][1000 genomes]
rs1771479	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1771482	0.94[EUR][1000 genomes]
rs1771483	0.94[EUR][1000 genomes]
rs1771484	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1771485	0.94[EUR][1000 genomes]
rs1771487	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2185544	0.82[EUR][1000 genomes]
rs2313601	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2776845	0.95[EUR][1000 genomes]
rs2776853	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2776855	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2776856	0.95[EUR][1000 genomes]
rs2792984	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2872538	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2989563	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3121188	0.81[EUR][1000 genomes]
rs3121190	0.85[EUR][1000 genomes]
rs3121191	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3121192	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3795777	0.92[EUR][1000 genomes]
rs3795782	0.88[EUR][1000 genomes]
rs3795795	0.91[ASN][1000 genomes]
rs3795801	0.91[ASN][1000 genomes]
rs45473794	0.83[ASN][1000 genomes]
rs4653543	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653545	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653549	0.91[ASN][1000 genomes]
rs4653931	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4653934	0.89[EUR][1000 genomes]
rs4653935	0.91[ASN][1000 genomes]
rs4653936	0.91[ASN][1000 genomes]
rs4653941	0.91[ASN][1000 genomes]
rs474735	0.92[ASN][1000 genomes]
rs489926	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs491293	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs493945	0.82[EUR][1000 genomes]
rs504474	0.92[ASN][1000 genomes]
rs512406	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs535329	0.92[ASN][1000 genomes]
rs545313	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs546967	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55658545	0.85[EUR][1000 genomes]
rs55971985	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56021350	0.91[ASN][1000 genomes]
rs56112646	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56168609	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs566640	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61825279	0.85[EUR][1000 genomes]
rs61825301	0.91[ASN][1000 genomes]
rs61825302	0.91[ASN][1000 genomes]
rs61825308	0.91[ASN][1000 genomes]
rs61827540	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6661539	0.82[EUR][1000 genomes]
rs72757829	0.83[EUR][1000 genomes]
rs7525075	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7532141	0.87[EUR][1000 genomes]
rs7532924	0.83[EUR][1000 genomes]
rs936884	0.92[ASN][1000 genomes]
rs947087	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
3	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
5	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
6	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
7	nsv827019	chr1:228314167-228651020	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
8	nsv1012078	chr1:228340876-228521843	Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
9	nsv535320	chr1:228340876-228521843	Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
10	nsv873263	chr1:228391808-228494790	Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
11	nsv873264	chr1:228423647-228543800	Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
12	nsv520340	chr1:228423936-228456147	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
13	nsv873265	chr1:228434395-228525008	Active TSS Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
14	nsv873266	chr1:228434395-228537942	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
15	nsv873267	chr1:228434395-228585837	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
16	nsv873268	chr1:228442663-228537942	Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
17	nsv873269	chr1:228442663-228543800	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
18	nsv873270	chr1:228442663-228699477	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4653933	OBSCN	cis	Skin Sun Exposed Lower leg	GTEx
rs4653933	OBSCN	cis	Esophagus Mucosa	GTEx

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228430600-228447000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr1:228433400-228449400	Weak transcription	Brain Anterior Caudate	brain
3	chr1:228434600-228455400	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr1:228434800-228445800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:228434800-228460000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:228434800-228462400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr1:228435000-228446000	Weak transcription	A549	lung
8	chr1:228435200-228449400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr1:228435200-228449600	Strong transcription	Primary T cells from cord blood	blood
10	chr1:228435200-228462800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr1:228435600-228462600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr1:228435800-228446400	Weak transcription	Fetal Heart	heart
13	chr1:228435800-228450200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr1:228436800-228447000	Weak transcription	Psoas Muscle	Psoas
15	chr1:228437000-228455600	Weak transcription	Hela-S3	cervix
16	chr1:228438400-228447000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr1:228438400-228455600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr1:228439200-228445200	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr1:228439200-228449400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:228439800-228448800	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr1:228440200-228447000	Weak transcription	Right Atrium	heart
22	chr1:228441200-228450400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:228442600-228448200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:228443000-228449200	Strong transcription	Right Ventricle	heart
25	chr1:228443000-228449400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:228443200-228454800	Strong transcription	Left Ventricle	heart
27	chr1:228443400-228445200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:228443400-228445600	Strong transcription	Fetal Muscle Leg	muscle
29	chr1:228443400-228446200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr1:228443400-228446200	Strong transcription	Fetal Muscle Trunk	muscle
31	chr1:228443400-228447000	Strong transcription	Fetal Lung	lung
32	chr1:228443400-228447000	Strong transcription	Thymus	Thymus
33	chr1:228443400-228448000	ZNF genes & repeats	Fetal Stomach	stomach
34	chr1:228443400-228449200	ZNF genes & repeats	Fetal Intestine Small	intestine
35	chr1:228443400-228449400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr1:228443400-228449800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:228443600-228462800	Weak transcription	Fetal Kidney	kidney
38	chr1:228443800-228447400	ZNF genes & repeats	Brain Germinal Matrix	brain
39	chr1:228443800-228449000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr1:228444000-228445200	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr1:228444000-228445200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr1:228444000-228448000	Strong transcription	HSMMtube	muscle
43	chr1:228444000-228461400	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr1:228444200-228447000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr1:228444200-228461600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr1:228444400-228447000	Weak transcription	Ovary	ovary
47	chr1:228444400-228450000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
48	chr1:228444600-228447000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr1:228444600-228447200	Weak transcription	Fetal Intestine Large	intestine
50	chr1:228444600-228450000	ZNF genes & repeats	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links