Variant report

Variant	rs17025339
Chromosome Location	chr2:98610621-98610622
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:98523325..98524831-chr2:98610615..98613167,2	MCF-7	breast:
2	chr2:98610350..98614892-chr2:98700211..98704879,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000075568	Chromatin interaction
ENSG00000168658	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11892146	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11895466	1.00[AMR][1000 genomes]
rs11898394	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11900781	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11900903	1.00[AMR][1000 genomes]
rs1503201	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1503203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17022209	1.00[AMR][1000 genomes]
rs17022289	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17022557	1.00[AMR][1000 genomes]
rs17022726	1.00[AMR][1000 genomes]
rs17022736	1.00[AMR][1000 genomes]
rs35774346	0.82[AFR][1000 genomes]
rs57434542	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58187838	1.00[AMR][1000 genomes]
rs60828800	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60885334	1.00[AMR][1000 genomes]
rs61712471	1.00[AMR][1000 genomes]
rs6543226	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6726775	1.00[ASW][hapmap];0.81[LWK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6734701	1.00[AMR][1000 genomes]
rs6736475	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6737992	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6742955	1.00[YRI][hapmap]
rs6746457	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942824	1.00[AMR][1000 genomes]
rs72942830	1.00[AMR][1000 genomes]
rs72942834	1.00[AMR][1000 genomes]
rs72942836	1.00[AMR][1000 genomes]
rs72942856	1.00[AMR][1000 genomes]
rs72942862	1.00[AMR][1000 genomes]
rs72942871	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942872	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942876	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942885	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942894	0.82[AFR][1000 genomes]
rs72942896	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942898	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944808	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944812	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944813	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944818	0.90[AFR][1000 genomes]
rs72944825	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944834	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944842	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946409	1.00[AMR][1000 genomes]
rs72946417	1.00[AMR][1000 genomes]
rs72946421	1.00[AMR][1000 genomes]
rs72946425	1.00[AMR][1000 genomes]
rs72946431	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946447	1.00[AMR][1000 genomes]
rs72946448	1.00[AMR][1000 genomes]
rs72946453	1.00[AMR][1000 genomes]
rs7579764	1.00[AMR][1000 genomes]
rs9308889	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526360	chr2:98403683-98814054	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv521568	chr2:98403683-98826203	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1004220	chr2:98423421-98816010	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1007259	chr2:98429744-98818080	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv535832	chr2:98429744-98818080	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1009218	chr2:98442640-98816010	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1003925	chr2:98442640-98821102	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv999442	chr2:98448732-98816010	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1013902	chr2:98454309-98818080	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv1013416	chr2:98472701-98688729	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv518056	chr2:98586842-99156296	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98600200-98611600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:98606200-98611200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr2:98606200-98611200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr2:98606400-98611000	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr2:98608200-98611400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:98608200-98611400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:98608200-98611400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:98608200-98611400	Weak transcription	Lung	lung
9	chr2:98608200-98611600	Weak transcription	Spleen	Spleen
10	chr2:98608400-98610800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr2:98608400-98611000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr2:98608600-98612800	Active TSS	GM12878-XiMat	blood
13	chr2:98609200-98613400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:98609400-98610800	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr2:98609400-98610800	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr2:98609400-98610800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
17	chr2:98609400-98610800	Enhancers	Fetal Heart	heart
18	chr2:98609400-98610800	Flanking Active TSS	NHDF-Ad	bronchial
19	chr2:98609400-98611000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:98609400-98611000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr2:98609400-98611000	Flanking Active TSS	NHEK	skin
22	chr2:98609400-98611400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr2:98609400-98613000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr2:98609400-98613200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr2:98609600-98611000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr2:98609800-98610800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr2:98609800-98610800	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr2:98609800-98610800	Flanking Active TSS	Brain Hippocampus Middle	brain
29	chr2:98609800-98610800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
30	chr2:98609800-98610800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
31	chr2:98609800-98611000	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr2:98609800-98611000	Flanking Active TSS	HepG2	liver
33	chr2:98609800-98611000	Flanking Active TSS	Osteobl	bone
34	chr2:98609800-98611200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:98609800-98611200	Flanking Active TSS	Brain Anterior Caudate	brain
36	chr2:98609800-98611200	Flanking Active TSS	Duodenum Mucosa	Duodenum
37	chr2:98609800-98611400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr2:98609800-98611400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr2:98609800-98611400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr2:98609800-98611600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr2:98609800-98612000	Flanking Active TSS	Primary B cells from cord blood	blood
42	chr2:98609800-98612800	Active TSS	NHLF	lung
43	chr2:98609800-98613200	Active TSS	Aorta	Aorta
44	chr2:98609800-98613400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr2:98610000-98610800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
46	chr2:98610000-98610800	Enhancers	Primary T cells fromperipheralblood	blood
47	chr2:98610000-98610800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr2:98610000-98610800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr2:98610000-98610800	Flanking Active TSS	Psoas Muscle	Psoas
50	chr2:98610000-98611000	Flanking Active TSS	Brain Germinal Matrix	brain

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