Variant report

Variant	rs58273936
Chromosome Location	chr2:11832780-11832781
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:11827607..11830089-chr2:11831192..11833222,2	K562	blood:
2	chr2:11832559..11835214-chr2:11848775..11850407,2	MCF-7	breast:
3	chr2:11826228..11828795-chr2:11831285..11833556,4	MCF-7	breast:
4	chr2:11828589..11830504-chr2:11831137..11833222,3	K562	blood:
5	chr2:11832764..11833679-chr2:11919280..11919852,3	MCF-7	breast:
6	chr2:11832588..11833837-chr2:11918873..11919890,5	MCF-7	breast:
7	chr2:11821317..11823796-chr2:11831362..11833008,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228496	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11890286	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28584687	0.89[ASN][1000 genomes]
rs4233903	0.83[EUR][1000 genomes]
rs55676775	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56858654	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57456819	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58454451	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs59502453	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59838011	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61410870	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61430487	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6432234	1.00[ASN][1000 genomes]
rs67334974	0.89[ASN][1000 genomes]
rs6754255	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6757729	0.83[EUR][1000 genomes]
rs73177496	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73179361	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73179363	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73179396	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73179398	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73181372	0.81[EUR][1000 genomes]
rs73181378	0.91[EUR][1000 genomes]
rs7556803	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7580386	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7580501	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7581186	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7581192	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7583977	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7583991	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7594198	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7594406	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7597552	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7597790	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7598255	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7598525	1.00[ASN][1000 genomes]
rs7601181	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7606137	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7606378	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7606724	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv1003899	chr2:11789374-12248081	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
4	nsv469449	chr2:11808654-11854012	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv580972	chr2:11808654-11854012	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv527025	chr2:11823585-11833459	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	esv10240	chr2:11832427-11837975	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11828800-11833400	Weak transcription	Colonic Mucosa	Colon
2	chr2:11828800-11833400	Weak transcription	Pancreas	Pancrea
3	chr2:11828800-11836800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:11829000-11833200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr2:11829000-11833200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr2:11829000-11833200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr2:11829000-11836600	Weak transcription	Fetal Thymus	thymus
8	chr2:11829000-11836600	Weak transcription	Right Atrium	heart
9	chr2:11829000-11836800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:11829200-11833000	Weak transcription	Primary B cells from peripheral blood	blood
11	chr2:11829200-11833000	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr2:11829200-11833000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr2:11829200-11833000	Weak transcription	Liver	Liver
14	chr2:11829200-11833200	Weak transcription	Placenta	Placenta
15	chr2:11829200-11833200	Weak transcription	K562	blood
16	chr2:11829200-11833400	Weak transcription	Duodenum Mucosa	Duodenum
17	chr2:11829200-11833400	Weak transcription	Fetal Intestine Large	intestine
18	chr2:11829200-11836000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr2:11829200-11836400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr2:11829200-11836600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr2:11829200-11836600	Weak transcription	Brain Hippocampus Middle	brain
22	chr2:11829200-11836800	Weak transcription	HUVEC	blood vessel
23	chr2:11829200-11837000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr2:11829200-11837000	Weak transcription	HSMM	muscle
25	chr2:11829200-11838400	Weak transcription	Fetal Lung	lung
26	chr2:11829400-11833200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr2:11829400-11833200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr2:11829400-11833200	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr2:11829400-11833200	Weak transcription	Fetal Muscle Leg	muscle
30	chr2:11829400-11833200	Weak transcription	Ovary	ovary
31	chr2:11829400-11833200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr2:11829400-11833200	Weak transcription	Stomach Smooth Muscle	stomach
33	chr2:11829400-11833200	Weak transcription	A549	lung
34	chr2:11829400-11833200	Weak transcription	Dnd41	blood
35	chr2:11829400-11833200	Weak transcription	NHDF-Ad	bronchial
36	chr2:11829400-11836400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:11829400-11836600	Weak transcription	Brain Anterior Caudate	brain
38	chr2:11829400-11836600	Weak transcription	NHEK	skin
39	chr2:11829400-11836800	Weak transcription	Brain Substantia Nigra	brain
40	chr2:11829400-11836800	Weak transcription	Colon Smooth Muscle	Colon
41	chr2:11829400-11837000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr2:11829400-11837000	Weak transcription	Fetal Heart	heart
43	chr2:11829400-11841800	Weak transcription	Primary B cells from cord blood	blood
44	chr2:11829600-11833200	Weak transcription	Hela-S3	cervix
45	chr2:11829600-11833400	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr2:11831000-11833000	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr2:11831400-11833800	Enhancers	Adipose Nuclei	Adipose
48	chr2:11831800-11835200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr2:11832000-11833800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:11832200-11833200	Weak transcription	Primary monocytes fromperipheralblood	blood

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