Variant report

Variant	rs58546246
Chromosome Location	chr2:98521823-98521824
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:98519788..98522524-chr2:98522979..98525608,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000075568	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10432626	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11678558	0.81[AMR][1000 genomes]
rs11678591	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11679828	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11680018	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11680321	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11680883	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11681535	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11684749	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11688829	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11690687	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11690737	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11691494	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11692010	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11692470	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12052222	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12052836	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12052846	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12104810	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12988571	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12995673	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13004090	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13006932	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13008968	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13020776	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13023980	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13028954	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13032265	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13032883	0.86[EUR][1000 genomes]
rs13034929	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1470483	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17488897	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17489454	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17489915	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17489984	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17490429	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1838797	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1875699	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2044458	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2044459	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2084176	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2278700	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2305143	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2871183	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3192177	0.81[AMR][1000 genomes]
rs3198055	0.83[EUR][1000 genomes]
rs34149969	0.83[EUR][1000 genomes]
rs34373359	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34502870	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34503448	0.85[EUR][1000 genomes]
rs34528940	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34654057	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34974566	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35098301	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35218942	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35255677	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35424768	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35505530	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35564270	0.84[EUR][1000 genomes]
rs35783535	0.86[EUR][1000 genomes]
rs4311104	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55776387	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55886305	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57681139	0.88[ASN][1000 genomes]
rs62156511	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6710088	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6711101	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6738389	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6746768	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6748124	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6757357	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71412824	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71429376	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs717417	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7421146	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7564773	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7583868	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7601898	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs895438	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs953320	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98503600-98522800	Weak transcription	HUVEC	blood vessel
2	chr2:98503800-98522600	Weak transcription	Fetal Kidney	kidney
3	chr2:98503800-98522800	Weak transcription	K562	blood
4	chr2:98503800-98524800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr2:98503800-98528600	Weak transcription	NHDF-Ad	bronchial
6	chr2:98503800-98536400	Weak transcription	HSMMtube	muscle
7	chr2:98504000-98522000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:98504000-98522200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:98504000-98522400	Weak transcription	Primary B cells from cord blood	blood
10	chr2:98504000-98522800	Weak transcription	Fetal Brain Female	brain
11	chr2:98504000-98523000	Weak transcription	Psoas Muscle	Psoas
12	chr2:98504000-98523600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr2:98504000-98528000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr2:98504000-98533800	Weak transcription	Spleen	Spleen
15	chr2:98504000-98538800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr2:98504000-98540600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr2:98504000-98540800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr2:98504200-98522200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr2:98504200-98522200	Weak transcription	Fetal Stomach	stomach
20	chr2:98504200-98522200	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr2:98504200-98522400	Weak transcription	Ovary	ovary
22	chr2:98504200-98522800	Weak transcription	Fetal Muscle Leg	muscle
23	chr2:98504200-98523000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr2:98504200-98523000	Weak transcription	Left Ventricle	heart
25	chr2:98504200-98525400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr2:98504200-98530800	Weak transcription	Thymus	Thymus
27	chr2:98504400-98522000	Weak transcription	Placenta	Placenta
28	chr2:98504400-98522800	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr2:98504400-98527000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr2:98504600-98522000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:98504600-98522200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr2:98504600-98522200	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr2:98504600-98522400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:98504600-98522400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr2:98504600-98522400	Weak transcription	Fetal Muscle Trunk	muscle
36	chr2:98504600-98522400	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr2:98504600-98522800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr2:98504600-98523000	Weak transcription	Brain Hippocampus Middle	brain
39	chr2:98504600-98523000	Weak transcription	Dnd41	blood
40	chr2:98504600-98523200	Weak transcription	Liver	Liver
41	chr2:98504600-98524200	Weak transcription	Adipose Nuclei	Adipose
42	chr2:98504600-98524200	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr2:98504600-98525600	Weak transcription	Duodenum Mucosa	Duodenum
44	chr2:98504600-98540800	Weak transcription	Stomach Smooth Muscle	stomach
45	chr2:98504600-98552200	Weak transcription	NHLF	lung
46	chr2:98504800-98527400	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr2:98505000-98523400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr2:98505200-98522200	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr2:98505400-98522000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr2:98505400-98522800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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