Variant report

Variant	rs2999129
Chromosome Location	chr1:59361652-59361653
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:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-JUN-2	chr1:59361517-59361681	ENSG00000232453
2	lnc-JUN-2	chr1:59361517-59361681	NONHSAT003536

Variant related genes	Relation type
ENSG00000177606	Chromatin interaction
ENSG00000234807	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs17096897	0.89[MEX][hapmap]
rs1998761	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1998762	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2011623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2492321	0.82[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap];0.91[MKK][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2492323	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2716117	0.80[ASW][hapmap];0.86[MKK][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes]
rs2764903	0.92[AFR][1000 genomes]
rs2764908	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2764909	0.82[ASW][hapmap];0.89[MEX][hapmap]

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

No data

Chromatin state (count:93 , 50 per page) page: 1 2

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	chr1:59358600-59361800	Enhancers	Gastric	stomach
6	chr1:59358600-59367000	Enhancers	Adipose Nuclei	Adipose
7	chr1:59358800-59365800	Enhancers	Lung	lung
8	chr1:59358800-59367000	Enhancers	Fetal Muscle Leg	muscle
9	chr1:59359000-59363000	Enhancers	Fetal Muscle Trunk	muscle
10	chr1:59359000-59363600	Enhancers	Pancreas	Pancrea
11	chr1:59359000-59363800	Enhancers	Right Ventricle	heart
12	chr1:59359000-59365800	Enhancers	Left Ventricle	heart
13	chr1:59359000-59366400	Enhancers	Primary hematopoietic stem cells	blood
14	chr1:59359000-59367000	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr1:59359000-59367200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr1:59359000-59368600	Enhancers	Fetal Intestine Small	intestine
17	chr1:59359000-59368800	Enhancers	Fetal Intestine Large	intestine
18	chr1:59359200-59366400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:59359400-59361800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:59359400-59361800	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr1:59359600-59365600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr1:59359600-59365600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr1:59359800-59363000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr1:59360000-59361800	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr1:59360000-59367000	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr1:59360600-59362400	Enhancers	Colon Smooth Muscle	Colon
27	chr1:59360600-59362800	Enhancers	Primary B cells from peripheral blood	blood
28	chr1:59360600-59362800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr1:59360600-59363200	Enhancers	Primary B cells from cord blood	blood
30	chr1:59360600-59363200	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr1:59360600-59363600	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr1:59360600-59364400	Enhancers	HepG2	liver
33	chr1:59360600-59365400	Enhancers	Spleen	Spleen
34	chr1:59360600-59366600	Enhancers	Colonic Mucosa	Colon
35	chr1:59360800-59361800	Enhancers	Muscle Satellite Cultured Cells	--
36	chr1:59360800-59361800	Enhancers	HMEC	breast
37	chr1:59360800-59362000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr1:59360800-59362000	Enhancers	HSMMtube	muscle
39	chr1:59360800-59362200	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr1:59360800-59362400	Enhancers	Liver	Liver
41	chr1:59360800-59362400	Enhancers	Hela-S3	cervix
42	chr1:59360800-59362600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr1:59360800-59362600	Enhancers	Primary T cells fromperipheralblood	blood
44	chr1:59360800-59362600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr1:59360800-59362600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
46	chr1:59360800-59362800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr1:59360800-59362800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:59360800-59362800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr1:59360800-59362800	Enhancers	Fetal Thymus	thymus
50	chr1:59360800-59362800	Enhancers	Small Intestine	intestine

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