Variant report

Variant	rs17459574
Chromosome Location	chr2:208839521-208839522
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	chr2:208632700..208635558-chr2:208837353..208840750,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163251	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12465292	0.93[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12471242	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13431014	0.93[CEU][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1452521	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17459758	0.93[CEU][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17537670	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17538061	1.00[YRI][hapmap]
rs28463196	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4502388	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62190863	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62190896	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62190898	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62190900	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62190904	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62190905	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62192772	0.82[AMR][1000 genomes]
rs6435402	0.93[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6740362	0.93[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72969822	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7565251	0.84[CEU][hapmap];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7588162	0.87[CEU][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs930745	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010531	chr2:208610639-209176782	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv536130	chr2:208610639-209176782	Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv875743	chr2:208688648-208940023	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv534496	chr2:208814372-209302791	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:208810400-208841000	Weak transcription	Fetal Lung	lung
2	chr2:208815400-208840800	Weak transcription	Ovary	ovary
3	chr2:208825200-208841400	Weak transcription	Aorta	Aorta
4	chr2:208825600-208841400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr2:208826600-208841400	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr2:208826800-208840800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr2:208827200-208841400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:208827200-208841400	Weak transcription	Pancreas	Pancrea
9	chr2:208827400-208841400	Weak transcription	Left Ventricle	heart
10	chr2:208827400-208841400	Weak transcription	Lung	lung
11	chr2:208827400-208857400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:208827800-208840800	Weak transcription	Fetal Muscle Leg	muscle
13	chr2:208828000-208840800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr2:208828000-208841000	Weak transcription	Fetal Thymus	thymus
15	chr2:208828200-208840400	Weak transcription	Thymus	Thymus
16	chr2:208828200-208841400	Weak transcription	Dnd41	blood
17	chr2:208832800-208841400	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr2:208834000-208842600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr2:208834000-208864000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr2:208834800-208865000	Weak transcription	HSMMtube	muscle
21	chr2:208835000-208840800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr2:208835000-208841200	Weak transcription	Fetal Stomach	stomach
23	chr2:208835200-208840800	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr2:208835600-208840800	Weak transcription	Primary T cells from cord blood	blood
25	chr2:208835600-208840800	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr2:208835600-208840800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr2:208835600-208840800	Weak transcription	K562	blood
28	chr2:208835600-208841200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr2:208835600-208841400	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr2:208835600-208841400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr2:208835600-208841400	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr2:208835600-208843200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr2:208835600-208846600	Weak transcription	Primary hematopoietic stem cells	blood
34	chr2:208835800-208840800	Weak transcription	Primary B cells from peripheral blood	blood
35	chr2:208835800-208840800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:208835800-208840800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr2:208835800-208840800	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr2:208835800-208841200	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr2:208835800-208841400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr2:208835800-208841400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr2:208835800-208841400	Weak transcription	Colonic Mucosa	Colon
42	chr2:208835800-208841400	Weak transcription	Colon Smooth Muscle	Colon
43	chr2:208835800-208841400	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr2:208835800-208841400	Weak transcription	Gastric	stomach
45	chr2:208835800-208841400	Weak transcription	Right Ventricle	heart
46	chr2:208835800-208855400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr2:208835800-208860800	Weak transcription	Small Intestine	intestine
48	chr2:208836000-208840800	Weak transcription	Brain Hippocampus Middle	brain
49	chr2:208836000-208840800	Weak transcription	Fetal Brain Female	brain
50	chr2:208836000-208841000	Weak transcription	Brain Germinal Matrix	brain

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