Variant report

Variant	rs12082896
Chromosome Location	chr1:59407776-59407777
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:59246467..59248452-chr1:59407731..59410394,2	K562	blood:
2	chr1:59407261..59409763-chr1:59434793..59436501,2	K562	blood:
3	chr1:59248910..59251256-chr1:59406675..59408781,2	K562	blood:
4	chr1:59246952..59251848-chr1:59405165..59409884,6	K562	blood:
5	chr1:59401291..59404305-chr1:59406315..59409384,3	MCF-7	breast:
6	chr1:59403568..59405263-chr1:59405379..59408693,3	K562	blood:

Variant related genes	Relation type
ENSG00000234807	Chromatin interaction
ENSG00000177606	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10889124	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11207335	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11207336	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11207337	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11207338	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11207341	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11207342	0.87[AFR][1000 genomes]
rs11207343	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12059773	1.00[MEX][hapmap]
rs12060581	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12070905	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12091374	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12092950	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12098063	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1323287	1.00[MEX][hapmap]
rs1331750	1.00[MEX][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

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59399200-59409400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:59402600-59408400	Weak transcription	A549	lung
3	chr1:59403200-59408000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:59403200-59408200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:59403200-59408200	Weak transcription	NHEK	skin
6	chr1:59403400-59408000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:59403400-59408200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:59403400-59408200	Weak transcription	HMEC	breast
9	chr1:59405400-59410800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:59406200-59407800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr1:59406600-59408200	Enhancers	Primary hematopoietic stem cells	blood
12	chr1:59406600-59408600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:59406600-59409200	Enhancers	Primary B cells from cord blood	blood
14	chr1:59406600-59410600	Enhancers	Primary B cells from peripheral blood	blood
15	chr1:59406600-59410800	Enhancers	Fetal Thymus	thymus
16	chr1:59406800-59407800	Enhancers	Esophagus	oesophagus
17	chr1:59406800-59408400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
18	chr1:59406800-59408600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
19	chr1:59406800-59409000	Enhancers	Adipose Nuclei	Adipose
20	chr1:59407000-59407800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
21	chr1:59407000-59407800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr1:59407000-59407800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:59407000-59407800	Enhancers	Thymus	Thymus
24	chr1:59407000-59408000	Enhancers	Spleen	Spleen
25	chr1:59407000-59408200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
26	chr1:59407000-59408400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
27	chr1:59407000-59408600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
28	chr1:59407000-59408600	Enhancers	HepG2	liver
29	chr1:59407000-59409000	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr1:59407000-59410400	Enhancers	Pancreas	Pancrea
31	chr1:59407200-59407800	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr1:59407200-59407800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
33	chr1:59407200-59407800	Enhancers	Liver	Liver
34	chr1:59407200-59407800	Enhancers	GM12878-XiMat	blood
35	chr1:59407200-59408000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
36	chr1:59407200-59408000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
37	chr1:59407200-59408200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
38	chr1:59407200-59408200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr1:59407200-59408400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
40	chr1:59407200-59408400	Enhancers	Fetal Lung	lung
41	chr1:59407200-59408600	Flanking Active TSS	Primary T cells from cord blood	blood
42	chr1:59407200-59409000	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr1:59407200-59409200	Enhancers	Duodenum Mucosa	Duodenum
44	chr1:59407200-59410000	Enhancers	Monocytes-CD14+_RO01746	blood
45	chr1:59407400-59408200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr1:59407400-59408200	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr1:59407400-59409000	Weak transcription	Small Intestine	intestine
48	chr1:59407400-59409000	Enhancers	Dnd41	blood
49	chr1:59407400-59409200	Enhancers	Rectal Mucosa Donor 29	rectum
50	chr1:59407400-59410200	Weak transcription	Colonic Mucosa	Colon

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