Variant report

Variant	rs3015311
Chromosome Location	chr1:59362218-59362219
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:59242448..59252747-chr1:59356992..59375072,48	K562	blood:
2	chr1:59242448..59251438-chr1:59358057..59375559,39	K562	blood:

Variant related genes	Relation type
ENSG00000234807	Chromatin interaction
ENSG00000177606	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10789072	0.86[JPT][hapmap]
rs10889121	0.85[JPT][hapmap]
rs12142126	0.81[JPT][hapmap]
rs1536159	0.82[JPT][hapmap]
rs2716105	1.00[CEU][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2716107	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2716113	0.86[JPT][hapmap]
rs2716115	0.83[MEX][hapmap]
rs2716120	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2764911	0.81[JPT][hapmap];0.82[MEX][hapmap]
rs2764914	0.86[JPT][hapmap]
rs2764915	0.82[MEX][hapmap]
rs3015312	0.81[JPT][hapmap]
rs4528141	0.80[CEU][hapmap];0.84[JPT][hapmap]
rs4912382	0.86[JPT][hapmap]
rs6661505	0.81[CHD][hapmap]
rs72921515	0.80[EUR][1000 genomes]
rs927743	0.82[CEU][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];0.96[MEX][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3015311	OMA1	cis	parietal	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59356200-59368600	Weak transcription	Esophagus	oesophagus
2	chr1:59357800-59364200	Enhancers	K562	blood
3	chr1:59358200-59367200	Enhancers	HUVEC	blood vessel
4	chr1:59358400-59368600	Enhancers	Rectal Mucosa Donor 31	rectum
5	chr1:59358600-59367000	Enhancers	Adipose Nuclei	Adipose
6	chr1:59358800-59365800	Enhancers	Lung	lung
7	chr1:59358800-59367000	Enhancers	Fetal Muscle Leg	muscle
8	chr1:59359000-59363000	Enhancers	Fetal Muscle Trunk	muscle
9	chr1:59359000-59363600	Enhancers	Pancreas	Pancrea
10	chr1:59359000-59363800	Enhancers	Right Ventricle	heart
11	chr1:59359000-59365800	Enhancers	Left Ventricle	heart
12	chr1:59359000-59366400	Enhancers	Primary hematopoietic stem cells	blood
13	chr1:59359000-59367000	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr1:59359000-59367200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr1:59359000-59368600	Enhancers	Fetal Intestine Small	intestine
16	chr1:59359000-59368800	Enhancers	Fetal Intestine Large	intestine
17	chr1:59359200-59366400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:59359600-59365600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr1:59359600-59365600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:59359800-59363000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr1:59360000-59367000	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr1:59360600-59362400	Enhancers	Colon Smooth Muscle	Colon
23	chr1:59360600-59362800	Enhancers	Primary B cells from peripheral blood	blood
24	chr1:59360600-59362800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr1:59360600-59363200	Enhancers	Primary B cells from cord blood	blood
26	chr1:59360600-59363200	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr1:59360600-59363600	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr1:59360600-59364400	Enhancers	HepG2	liver
29	chr1:59360600-59365400	Enhancers	Spleen	Spleen
30	chr1:59360600-59366600	Enhancers	Colonic Mucosa	Colon
31	chr1:59360800-59362400	Enhancers	Liver	Liver
32	chr1:59360800-59362400	Enhancers	Hela-S3	cervix
33	chr1:59360800-59362600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:59360800-59362600	Enhancers	Primary T cells fromperipheralblood	blood
35	chr1:59360800-59362600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr1:59360800-59362600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
37	chr1:59360800-59362800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:59360800-59362800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr1:59360800-59362800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:59360800-59362800	Enhancers	Fetal Thymus	thymus
41	chr1:59360800-59362800	Enhancers	Small Intestine	intestine
42	chr1:59360800-59363000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:59360800-59363000	Enhancers	Fetal Stomach	stomach
44	chr1:59360800-59363200	Enhancers	Placenta Amnion	Placenta Amnion
45	chr1:59360800-59363200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr1:59360800-59363400	Enhancers	Brain Substantia Nigra	brain
47	chr1:59360800-59363600	Enhancers	Brain Anterior Caudate	brain
48	chr1:59360800-59363600	Enhancers	Psoas Muscle	Psoas
49	chr1:59360800-59363800	Enhancers	Brain Hippocampus Middle	brain
50	chr1:59360800-59364800	Enhancers	Right Atrium	heart

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