Variant report

Variant	rs2049400
Chromosome Location	chr2:100253159-100253160
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:31)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:31 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:100252895..100253779-chr2:100630036..100630900,5	MCF-7	breast:
2	chr2:100217748..100218713-chr2:100252975..100253496,2	MCF-7	breast:
3	chr2:100225923..100227094-chr2:100252804..100253814,22	MCF-7	breast:
4	chr2:100233720..100235123-chr2:100252828..100253769,13	MCF-7	breast:
5	chr2:100190245..100191307-chr2:100252548..100253839,102	MCF-7	breast:
6	chr2:100147596..100148577-chr2:100252771..100253795,14	MCF-7	breast:
7	chr2:100252844..100253666-chr2:100422970..100423881,3	MCF-7	breast:
8	chr2:100253013..100253774-chr2:100554553..100555389,2	MCF-7	breast:
9	chr2:100252751..100253728-chr2:100273126..100274127,6	MCF-7	breast:
10	chr2:100233994..100235115-chr2:100252752..100253859,38	MCF-7	breast:
11	chr2:100234012..100235039-chr2:100252791..100253859,26	MCF-7	breast:
12	chr2:100251850..100255492-chr2:100257476..100259432,3	K562	blood:
13	chr2:100252843..100253378-chr4:140590285..140590804,2	MCF-7	breast:
14	chr2:100190245..100191307-chr2:100252548..100253839,52	MCF-7	breast:
15	chr2:100147647..100148577-chr2:100252771..100253795,10	MCF-7	breast:
16	chr2:100252895..100253779-chr2:100630074..100630900,2	MCF-7	breast:
17	chr2:100252850..100253419-chr2:100672872..100673558,3	MCF-7	breast:
18	chr2:100190136..100191330-chr2:100252785..100253901,32	MCF-7	breast:
19	chr2:100225933..100226951-chr2:100252763..100253732,25	MCF-7	breast:
20	chr2:100147592..100148271-chr2:100252816..100253797,7	MCF-7	breast:
21	chr2:100193349..100195395-chr2:100253004..100255403,2	MCF-7	breast:
22	chr2:100236243..100237127-chr2:100252933..100253776,3	MCF-7	breast:
23	chr2:100252944..100253687-chr2:100678182..100678844,3	MCF-7	breast:
24	chr2:100252860..100253522-chr20:52739988..52740766,2	MCF-7	breast:
25	chr2:100252809..100253781-chr2:100678108..100678796,2	MCF-7	breast:
26	chr2:100225916..100227069-chr2:100252788..100253814,68	MCF-7	breast:
27	chr2:100252857..100253710-chr2:100883998..100884797,3	MCF-7	breast:
28	chr2:100252907..100253773-chr2:100884171..100885187,3	MCF-7	breast:
29	chr2:100252843..100253422-chr5:1032799..1033319,2	MCF-7	breast:
30	chr2:100252751..100253728-chr2:100273126..100274127,5	MCF-7	breast:
31	chr2:100218130..100218636-chr2:100252855..100253365,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000144218	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10167554	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11123790	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11684088	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12620982	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12712049	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12712054	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13029690	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1357719	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1996984	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2030691	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2030692	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2030693	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2177541	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2177542	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2309729	0.82[EUR][1000 genomes]
rs2871316	0.82[EUR][1000 genomes]
rs3792129	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3792130	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3792131	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4850910	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4851220	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4851221	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6542884	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6738724	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6745568	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6746146	0.80[EUR][1000 genomes]
rs7561009	0.82[EUR][1000 genomes]
rs7579222	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs868665	0.80[EUR][1000 genomes]
rs9284724	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9308826	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9308827	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9678859	0.92[AMR][1000 genomes];0.97[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	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv962113	chr2:100022168-100317461	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1003343	chr2:100241560-100848900	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv535843	chr2:100241560-100848900	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100217000-100258400	Weak transcription	Primary T cells from cord blood	blood
2	chr2:100238000-100253200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr2:100239600-100257200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr2:100251000-100254400	Enhancers	Adipose Nuclei	Adipose
5	chr2:100251200-100254000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr2:100251800-100254000	Enhancers	Left Ventricle	heart
7	chr2:100251800-100254400	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr2:100251800-100258400	Enhancers	Fetal Muscle Leg	muscle
9	chr2:100252000-100253600	Genic enhancers	Primary B cells from peripheral blood	blood
10	chr2:100252000-100254000	Enhancers	Pancreas	Pancrea
11	chr2:100252000-100254000	Enhancers	Right Atrium	heart
12	chr2:100252000-100254000	Enhancers	Spleen	Spleen
13	chr2:100252000-100254600	Enhancers	Thymus	Thymus
14	chr2:100252000-100254800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr2:100252000-100255200	Enhancers	Fetal Muscle Trunk	muscle
16	chr2:100252000-100256600	Enhancers	Fetal Thymus	thymus
17	chr2:100252200-100253600	Enhancers	Fetal Stomach	stomach
18	chr2:100252200-100253600	Enhancers	Psoas Muscle	Psoas
19	chr2:100252200-100253600	Enhancers	Stomach Smooth Muscle	stomach
20	chr2:100252200-100253800	Enhancers	Lung	lung
21	chr2:100252200-100254000	Enhancers	Brain Hippocampus Middle	brain
22	chr2:100252200-100254000	Enhancers	Colon Smooth Muscle	Colon
23	chr2:100252200-100254000	Enhancers	Right Ventricle	heart
24	chr2:100252400-100253200	Strong transcription	Primary hematopoietic stem cells	blood
25	chr2:100252400-100253200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr2:100252400-100253200	Strong transcription	Dnd41	blood
27	chr2:100252400-100253400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr2:100252400-100253600	Enhancers	Brain Cingulate Gyrus	brain
29	chr2:100252400-100253600	Enhancers	Brain Substantia Nigra	brain
30	chr2:100252400-100253800	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr2:100252400-100263800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr2:100252600-100253400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr2:100252600-100253600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr2:100252600-100253600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:100252600-100253600	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr2:100252600-100253600	Enhancers	Brain Anterior Caudate	brain
37	chr2:100252600-100253600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr2:100252600-100253800	Enhancers	Fetal Lung	lung
39	chr2:100252600-100254000	Enhancers	Liver	Liver
40	chr2:100252600-100254000	Enhancers	Brain Germinal Matrix	brain
41	chr2:100252800-100253200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr2:100252800-100253200	Enhancers	NHDF-Ad	bronchial
43	chr2:100252800-100253200	Enhancers	Osteobl	bone
44	chr2:100252800-100253400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr2:100252800-100253400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr2:100252800-100253800	Enhancers	Ovary	ovary
47	chr2:100252800-100254000	Enhancers	K562	blood
48	chr2:100252800-100254400	Enhancers	HSMMtube	muscle
49	chr2:100252800-100254600	Enhancers	Fetal Brain Male	brain
50	chr2:100253000-100253200	Weak transcription	Primary B cells from cord blood	blood

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