Variant report

Variant	rs2776853
Chromosome Location	chr1:228402508-228402509
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr1:228400727-228402575	IMR90	lung:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:228352301..228356055-chr1:228400478..228402839,5	K562	blood:
2	chr1:228352180..228354320-chr1:228400730..228402843,3	MCF-7	breast:
3	chr1:228401876..228404808-chr1:228460949..228463356,3	K562	blood:
4	chr1:228400118..228403034-chr1:228591844..228593875,2	MCF-7	breast:
5	chr1:228400987..228403639-chr1:228644070..228647036,3	K562	blood:
6	chr1:228401076..228403639-chr1:228645192..228647036,2	K562	blood:

No data

Variant related genes	Relation type
OBSCN	TF binding region
C1orf145	TF binding region
ENSG00000181218	Chromatin interaction
ENSG00000196890	Chromatin interaction
ENSG00000203684	Chromatin interaction
ENSG00000181873	Chromatin interaction
ENSG00000269890	Chromatin interaction
ENSG00000154370	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs1059778	0.87[EUR][1000 genomes]
rs10753445	0.88[EUR][1000 genomes]
rs10799468	0.84[EUR][1000 genomes]
rs10799469	0.80[EUR][1000 genomes]
rs10799471	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10916268	0.84[EUR][1000 genomes]
rs10916271	0.87[EUR][1000 genomes]
rs11580411	0.83[EUR][1000 genomes]
rs11584385	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11799681	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11804508	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12024649	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12118872	0.81[EUR][1000 genomes]
rs12726781	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12745416	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1331303	0.93[EUR][1000 genomes]
rs1411910	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1411911	0.83[EUR][1000 genomes]
rs1411913	0.83[EUR][1000 genomes]
rs1620111	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1629290	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1629294	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1757129	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1757132	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1757133	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1757138	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1757139	0.93[EUR][1000 genomes]
rs1757140	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1757141	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1757142	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1757144	0.94[EUR][1000 genomes]
rs1757145	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1757147	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1757148	0.95[EUR][1000 genomes]
rs1757149	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1757150	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1757151	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1757152	0.93[EUR][1000 genomes]
rs1757153	0.83[ASN][1000 genomes]
rs1757155	0.94[EUR][1000 genomes]
rs1757156	0.94[EUR][1000 genomes]
rs1757158	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17640616	0.84[EUR][1000 genomes]
rs1771459	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1771460	0.92[EUR][1000 genomes]
rs1771461	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1771462	0.94[EUR][1000 genomes]
rs1771467	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1771468	0.92[EUR][1000 genomes]
rs1771469	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1771470	0.93[EUR][1000 genomes]
rs1771471	0.94[EUR][1000 genomes]
rs1771472	0.94[EUR][1000 genomes]
rs1771474	0.95[EUR][1000 genomes]
rs1771476	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1771477	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1771478	0.94[EUR][1000 genomes]
rs1771479	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1771482	0.94[EUR][1000 genomes]
rs1771483	0.94[EUR][1000 genomes]
rs1771484	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1771485	0.96[EUR][1000 genomes]
rs1771487	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2185544	0.87[EUR][1000 genomes]
rs2313601	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2313602	0.84[EUR][1000 genomes]
rs2776845	0.94[EUR][1000 genomes]
rs2776855	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2776856	0.93[EUR][1000 genomes]
rs2792984	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2872538	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2989563	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3121188	0.86[EUR][1000 genomes]
rs3121190	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3121191	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3121192	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3795777	0.93[EUR][1000 genomes]
rs3795782	0.82[EUR][1000 genomes]
rs4653536	0.85[EUR][1000 genomes]
rs4653543	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4653545	0.91[EUR][1000 genomes]
rs4653915	0.83[EUR][1000 genomes]
rs4653931	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4653933	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4653934	0.83[EUR][1000 genomes]
rs489926	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs491293	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs512406	0.91[EUR][1000 genomes]
rs545313	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs546967	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55658545	0.84[EUR][1000 genomes]
rs55971985	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56112646	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56168609	0.80[EUR][1000 genomes]
rs566640	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61827540	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6661539	0.82[EUR][1000 genomes]
rs72757829	0.85[EUR][1000 genomes]
rs7512209	0.82[EUR][1000 genomes]
rs7525075	0.92[EUR][1000 genomes]
rs7532141	0.82[EUR][1000 genomes]
rs7532924	0.89[EUR][1000 genomes]
rs7537636	0.82[EUR][1000 genomes]
rs947087	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv873257	chr1:228322826-228412106	Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
9	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
10	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
11	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
12	esv3397989	chr1:228398279-228402677	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
13	esv3358379	chr1:228399204-228403102	Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2776853	OBSCN	cis	Skin Sun Exposed Lower leg	GTEx
rs2776853	OBSCN	cis	Esophagus Mucosa	GTEx

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228395800-228405200	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
2	chr1:228400000-228402600	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr1:228400200-228402600	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr1:228400400-228403200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:228400600-228404200	Active TSS	Brain Anterior Caudate	brain
6	chr1:228401400-228402600	Weak transcription	Primary T cells from cord blood	blood
7	chr1:228401400-228403800	Genic enhancers	Left Ventricle	heart
8	chr1:228401400-228404200	Enhancers	Fetal Brain Male	brain
9	chr1:228401400-228405200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:228401400-228412200	Weak transcription	HSMMtube	muscle
11	chr1:228401400-228412600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr1:228401600-228402600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:228401600-228412200	Weak transcription	Right Atrium	heart
14	chr1:228401800-228402600	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:228401800-228402600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:228401800-228402600	Enhancers	Pancreas	Pancrea
17	chr1:228401800-228402800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
18	chr1:228401800-228404400	Genic enhancers	Right Ventricle	heart
19	chr1:228401800-228407200	Weak transcription	Ovary	ovary
20	chr1:228401800-228412000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr1:228402000-228402600	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr1:228402000-228402600	Enhancers	Colonic Mucosa	Colon
23	chr1:228402000-228402600	Transcr. at gene 5' and 3'	Dnd41	blood
24	chr1:228402000-228402800	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr1:228402000-228402800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:228402000-228402800	Enhancers	Fetal Lung	lung
27	chr1:228402000-228403200	Enhancers	Primary T cells fromperipheralblood	blood
28	chr1:228402000-228404600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr1:228402000-228404600	Enhancers	Fetal Heart	heart
30	chr1:228402000-228405000	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
31	chr1:228402000-228406800	Weak transcription	Psoas Muscle	Psoas
32	chr1:228402000-228407200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr1:228402000-228407200	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr1:228402000-228412000	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr1:228402000-228412200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:228402000-228412200	Weak transcription	Duodenum Mucosa	Duodenum
37	chr1:228402000-228412600	Weak transcription	Fetal Kidney	kidney
38	chr1:228402200-228402600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:228402200-228402600	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr1:228402200-228402800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr1:228402200-228402800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr1:228402200-228402800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr1:228402200-228402800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr1:228402200-228402800	Enhancers	Esophagus	oesophagus
45	chr1:228402200-228402800	Genic enhancers	Thymus	Thymus
46	chr1:228402200-228403400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr1:228402200-228403400	Weak transcription	Fetal Intestine Large	intestine
48	chr1:228402200-228403600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr1:228402200-228403600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr1:228402200-228403600	Weak transcription	Gastric	stomach

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