Variant report

Variant	rs58560917
Chromosome Location	chr2:99419631-99419632
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	chr2:99408337..99412495-chr2:99418942..99424150,7	MCF-7	breast:
2	chr2:99419187..99420938-chr2:99424125..99425695,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs2090181	0.83[ASN][1000 genomes]
rs2203432	0.83[ASN][1000 genomes]
rs2871243	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2871244	0.83[ASN][1000 genomes]
rs3731660	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4851160	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs58676789	0.89[ASN][1000 genomes]
rs59083513	0.83[ASN][1000 genomes]
rs59313126	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs59989465	1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs60496162	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61042973	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61311613	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61359279	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61402919	0.83[ASN][1000 genomes]
rs72811003	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72811004	1.00[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs72811005	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72827717	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs72827722	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs72827724	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs72827727	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs72827729	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs72827731	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs72827732	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs72827733	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs72827734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs72827736	0.81[ASN][1000 genomes]
rs72827739	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72827740	0.83[ASN][1000 genomes]
rs72827741	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72827742	0.83[ASN][1000 genomes]
rs72827743	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[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	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99406000-99421800	Weak transcription	Spleen	Spleen
2	chr2:99407600-99423800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:99409200-99425800	Weak transcription	Small Intestine	intestine
4	chr2:99409600-99426400	Weak transcription	Esophagus	oesophagus
5	chr2:99410600-99421600	Weak transcription	Brain Hippocampus Middle	brain
6	chr2:99411200-99421200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr2:99411200-99421200	Weak transcription	Right Atrium	heart
8	chr2:99411200-99422200	Weak transcription	Colon Smooth Muscle	Colon
9	chr2:99412800-99421800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr2:99413800-99422000	Weak transcription	Duodenum Mucosa	Duodenum
11	chr2:99413800-99423800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr2:99414000-99426600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr2:99414200-99422200	Weak transcription	Fetal Intestine Large	intestine
14	chr2:99414600-99422000	Weak transcription	Fetal Brain Male	brain
15	chr2:99416000-99421200	Weak transcription	HMEC	breast
16	chr2:99416000-99421400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr2:99416200-99421800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr2:99416200-99421800	Weak transcription	Brain Substantia Nigra	brain
19	chr2:99416400-99421400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:99416400-99421800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr2:99416400-99422000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr2:99417600-99421000	Weak transcription	Left Ventricle	heart
23	chr2:99417600-99421800	Weak transcription	HUVEC	blood vessel
24	chr2:99417800-99420000	Weak transcription	Liver	Liver
25	chr2:99417800-99420800	Weak transcription	Fetal Heart	heart
26	chr2:99417800-99421600	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr2:99418000-99421800	Weak transcription	Right Ventricle	heart
28	chr2:99418000-99422200	Weak transcription	Psoas Muscle	Psoas
29	chr2:99418000-99442200	Weak transcription	Stomach Mucosa	stomach
30	chr2:99418200-99423800	Weak transcription	Thymus	Thymus
31	chr2:99418400-99420400	Weak transcription	Fetal Muscle Leg	muscle
32	chr2:99418400-99421600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr2:99418400-99421800	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr2:99418600-99419800	Weak transcription	HepG2	liver
35	chr2:99418600-99420000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:99418800-99419800	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr2:99418800-99420000	Weak transcription	Pancreas	Pancrea
38	chr2:99418800-99420200	Weak transcription	Fetal Thymus	thymus
39	chr2:99418800-99420200	Weak transcription	Lung	lung
40	chr2:99418800-99421800	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr2:99418800-99422200	Weak transcription	Gastric	stomach
42	chr2:99418800-99425000	Weak transcription	Fetal Intestine Small	intestine
43	chr2:99419400-99421200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr2:99419400-99421800	Weak transcription	Brain Anterior Caudate	brain

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