Variant report

Variant	rs927743
Chromosome Location	chr1:59368947-59368948
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:59368740..59369670-chr18:19284195..19284964,2	Hela-S3	cervix:
2	chr1:59366576..59370002-chr1:59372804..59375528,3	K562	blood:
3	chr1:59348233..59353011-chr1:59368695..59371190,6	K562	blood:
4	chr1:59361444..59363025-chr1:59368873..59370634,2	MCF-7	breast:
5	chr1:59242448..59252747-chr1:59356992..59375072,48	K562	blood:
6	chr1:59363087..59366662-chr1:59367277..59371776,8	K562	blood:
7	chr1:59360593..59363269-chr1:59368907..59370724,2	MCF-7	breast:
8	chr1:59322966..59325903-chr1:59367463..59369481,2	K562	blood:
9	chr1:59242448..59251438-chr1:59358057..59375559,39	K562	blood:
10	chr1:59248088..59252183-chr1:59365231..59372787,10	MCF-7	breast:
11	chr1:59247507..59253331-chr1:59366916..59371031,9	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000101752	Chromatin interaction
ENSG00000234807	Chromatin interaction
ENSG00000232453	Chromatin interaction
ENSG00000177606	Chromatin interaction
ENSG00000158201	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10493253	0.86[JPT][hapmap]
rs11207323	0.82[CHD][hapmap];0.82[JPT][hapmap]
rs11207326	0.82[JPT][hapmap]
rs12117564	0.82[CHD][hapmap];0.82[JPT][hapmap]
rs2716105	0.82[CEU][hapmap];0.85[CHD][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.80[EUR][1000 genomes]
rs2716107	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs2716115	0.85[CEU][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap]
rs2764911	0.84[MEX][hapmap]
rs2764914	0.80[MEX][hapmap]
rs2764915	0.85[CEU][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs2764917	0.85[CEU][hapmap];0.85[JPT][hapmap]
rs3015311	0.82[CEU][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];0.96[MEX][hapmap];0.81[EUR][1000 genomes]
rs6697107	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005354	chr1:59283572-59535812	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv829959	chr1:59340330-59503085	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv546316	chr1:59368947-59457815	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs927743	OMA1	cis	parietal	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59362400-59369000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr1:59362800-59369000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:59362800-59369000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:59363200-59369000	Weak transcription	Brain Angular Gyrus	brain
5	chr1:59365400-59369000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:59365400-59369000	Weak transcription	Right Ventricle	heart
7	chr1:59365400-59369200	Weak transcription	Gastric	stomach
8	chr1:59365600-59369000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr1:59365600-59369000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:59365600-59369000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:59366000-59369000	Weak transcription	Fetal Kidney	kidney
12	chr1:59366000-59369000	Enhancers	K562	blood
13	chr1:59366400-59369000	Weak transcription	Primary hematopoietic stem cells	blood
14	chr1:59366400-59369000	Weak transcription	Fetal Brain Male	brain
15	chr1:59366400-59369000	Weak transcription	Left Ventricle	heart
16	chr1:59366600-59369000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:59367000-59369000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr1:59367000-59369000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:59367000-59369000	Weak transcription	Ovary	ovary
20	chr1:59367000-59369000	Weak transcription	Psoas Muscle	Psoas
21	chr1:59367000-59369000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr1:59367200-59369000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr1:59367200-59369000	Weak transcription	HSMMtube	muscle
24	chr1:59368200-59369000	Enhancers	Fetal Muscle Trunk	muscle
25	chr1:59368400-59369000	Enhancers	Fetal Thymus	thymus
26	chr1:59368600-59369000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr1:59368600-59369000	Enhancers	Primary T cells fromperipheralblood	blood
28	chr1:59368600-59369000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr1:59368600-59369000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr1:59368600-59369000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:59368600-59369000	Enhancers	Colon Smooth Muscle	Colon
32	chr1:59368600-59369000	Enhancers	Esophagus	oesophagus
33	chr1:59368600-59369000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr1:59368600-59369000	Enhancers	Fetal Stomach	stomach
35	chr1:59368600-59369000	Enhancers	Lung	lung
36	chr1:59368600-59369200	Flanking Active TSS	Brain Anterior Caudate	brain
37	chr1:59368600-59369200	Flanking Active TSS	Fetal Intestine Small	intestine
38	chr1:59368600-59369200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
39	chr1:59368600-59369200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
40	chr1:59368600-59369200	Flanking Active TSS	HepG2	liver
41	chr1:59368600-59369400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
42	chr1:59368600-59369400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr1:59368600-59369400	Flanking Active TSS	Stomach Smooth Muscle	stomach
44	chr1:59368600-59369400	Flanking Active TSS	GM12878-XiMat	blood
45	chr1:59368600-59369400	Flanking Active TSS	Hela-S3	cervix
46	chr1:59368600-59369600	Enhancers	Placenta Amnion	Placenta Amnion
47	chr1:59368800-59369000	Active TSS	ES-I3 Cell Line	embryonic stem cell
48	chr1:59368800-59369000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
49	chr1:59368800-59369000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
50	chr1:59368800-59369000	Active TSS	Primary B cells from cord blood	blood

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