Variant report

Variant	rs17012834
Chromosome Location	chr3:23262290-23262291
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:23255785..23258216-chr3:23259980..23262399,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10510537	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13077333	0.94[ASN][1000 genomes]
rs13083654	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs13087234	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs13089963	0.90[ASN][1000 genomes]
rs13095887	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13095960	0.88[ASN][1000 genomes]
rs13098494	0.85[JPT][hapmap]
rs1495132	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17012823	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17012844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17012852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17012861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17012897	0.98[ASN][1000 genomes]
rs17012927	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17012943	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17012959	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17012969	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17012988	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17012998	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17013003	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs17013023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17013026	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17013029	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17013035	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17013049	0.81[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17013104	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17013116	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17013125	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17013128	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17013152	1.00[CEU][hapmap];0.88[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17345745	0.88[JPT][hapmap]
rs2014132	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2291720	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs34239585	0.98[ASN][1000 genomes]
rs34259979	0.98[ASN][1000 genomes]
rs34646795	0.90[ASN][1000 genomes]
rs35743404	0.98[ASN][1000 genomes]
rs36004369	0.94[ASN][1000 genomes]
rs58844120	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59365170	0.96[AMR][1000 genomes]
rs60709653	0.96[AMR][1000 genomes]
rs73044305	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs73044309	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs73044318	0.96[AMR][1000 genomes]
rs73044329	0.96[AMR][1000 genomes]
rs73044337	0.96[AMR][1000 genomes]
rs73044339	0.96[AMR][1000 genomes]
rs73050236	0.96[AMR][1000 genomes]
rs73050238	0.96[AMR][1000 genomes]
rs73050257	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs73050270	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs73050276	1.00[AMR][1000 genomes];0.83[ASN][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	nsv834636	chr3:23138653-23301443	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1014701	chr3:23257658-23416094	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23245800-23262800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:23246200-23264200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr3:23246400-23273400	Weak transcription	Aorta	Aorta
4	chr3:23246600-23262400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr3:23248800-23265800	Weak transcription	Primary T cells from cord blood	blood
6	chr3:23249000-23273400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr3:23251600-23262800	Weak transcription	Adipose Nuclei	Adipose
8	chr3:23257000-23263200	Enhancers	Brain Hippocampus Middle	brain
9	chr3:23259000-23262600	Enhancers	Colon Smooth Muscle	Colon
10	chr3:23259400-23262400	Enhancers	Liver	Liver
11	chr3:23260400-23262400	Enhancers	Osteobl	bone
12	chr3:23260600-23262400	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr3:23260800-23262600	Enhancers	Primary B cells from peripheral blood	blood
14	chr3:23260800-23262600	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr3:23260800-23270400	Weak transcription	Psoas Muscle	Psoas
16	chr3:23260800-23273400	Weak transcription	Right Atrium	heart
17	chr3:23261000-23262400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr3:23261000-23262600	Enhancers	Primary B cells from cord blood	blood
19	chr3:23261000-23273400	Weak transcription	Ovary	ovary
20	chr3:23261000-23274400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr3:23261200-23262400	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr3:23261200-23262600	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr3:23261200-23264800	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr3:23261200-23272600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr3:23261400-23262400	Weak transcription	Thymus	Thymus
26	chr3:23261400-23278200	Weak transcription	Brain Angular Gyrus	brain
27	chr3:23261600-23264400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr3:23262000-23263400	Flanking Active TSS	GM12878-XiMat	blood
29	chr3:23262200-23263200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood

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