Variant report

Variant	rs2280410
Chromosome Location	chr3:46599937-46599938
allele	C/T
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:46529825..46532011-chr3:46599266..46600570,56	K562	blood:
2	chr3:46537907..46538428-chr3:46599296..46599996,2	K562	blood:
3	chr3:46531009..46531629-chr3:46599490..46600081,2	MCF-7	breast:
4	chr3:46529686..46530942-chr3:46599020..46600485,46	MCF-7	breast:
5	chr3:46498573..46499197-chr3:46599063..46599998,2	K562	blood:
6	chr3:46529889..46530997-chr3:46599244..46600312,18	MCF-7	breast:
7	chr3:46537971..46538930-chr3:46599529..46600154,4	MCF-7	breast:
8	chr3:46537655..46538429-chr3:46599459..46599986,2	MCF-7	breast:
9	chr3:46599516..46600466-chr3:46671185..46672080,3	MCF-7	breast:
10	chr3:46599422..46601505-chr3:46601570..46603414,2	K562	blood:
11	chr3:46584414..46585245-chr3:46599503..46600045,2	K562	blood:

No data

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs17286758	0.81[CHB][hapmap]
rs2280408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280409	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2280414	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2293021	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2293022	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2293023	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2293024	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2293025	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28617572	0.84[ASN][1000 genomes]
rs28687398	0.81[ASN][1000 genomes]
rs3189859	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3806704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3827493	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4312690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55649212	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55693118	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55736632	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55763532	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55923987	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55955974	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55957516	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56008703	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56048308	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56163098	0.81[AMR][1000 genomes]
rs56168669	0.81[AMR][1000 genomes]
rs56188400	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56197743	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56394040	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56398705	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56695799	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58177689	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58551379	0.81[AMR][1000 genomes]
rs58572135	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59673973	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59836693	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6442003	0.81[CHB][hapmap]
rs6772291	0.81[CHB][hapmap]
rs6778422	0.81[CHB][hapmap]
rs73069984	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73069987	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73069989	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73069992	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73069996	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73069997	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73071917	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73071919	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73071930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73071938	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73072002	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73073704	0.81[ASN][1000 genomes]
rs73073732	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73073734	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73073742	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73073744	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73073745	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73073746	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73073750	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73073752	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73073753	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73073754	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73073755	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73075515	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73075519	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73075524	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73075528	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73075564	0.92[AMR][1000 genomes]
rs73075571	0.92[AMR][1000 genomes]
rs73077539	0.81[AMR][1000 genomes]
rs73077544	0.81[AMR][1000 genomes]
rs7648827	0.81[CHB][hapmap]
rs9808967	0.81[CHB][hapmap]
rs9846026	0.81[CHB][hapmap]
rs9871405	0.81[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013306	chr3:46469014-46698538	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46591400-46600200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:46591600-46600000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr3:46591800-46606600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:46593000-46600200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:46593200-46600000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:46593200-46600000	Weak transcription	Ovary	ovary
7	chr3:46597000-46600000	Enhancers	HUVEC	blood vessel
8	chr3:46597800-46600000	Enhancers	Muscle Satellite Cultured Cells	--
9	chr3:46597800-46600000	Enhancers	Hela-S3	cervix
10	chr3:46598400-46600000	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr3:46598400-46600000	Enhancers	HSMM	muscle
12	chr3:46598400-46600200	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr3:46598400-46601000	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr3:46598600-46600000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr3:46598600-46600000	Enhancers	NH-A	brain
16	chr3:46598800-46600000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:46598800-46600000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:46598800-46600000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:46598800-46600000	Enhancers	NHLF	lung
20	chr3:46598800-46600400	Enhancers	H1 Cell Line	embryonic stem cell
21	chr3:46599000-46600000	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr3:46599000-46600200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:46599000-46600400	Enhancers	Dnd41	blood
24	chr3:46599000-46601200	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr3:46599200-46600000	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr3:46599200-46600000	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr3:46599200-46600000	Enhancers	Fetal Thymus	thymus
28	chr3:46599200-46600000	Enhancers	Gastric	stomach
29	chr3:46599200-46600000	Enhancers	Left Ventricle	heart
30	chr3:46599200-46600000	Enhancers	Pancreas	Pancrea
31	chr3:46599200-46600000	Enhancers	Psoas Muscle	Psoas
32	chr3:46599200-46600000	Enhancers	Right Ventricle	heart
33	chr3:46599200-46600000	Enhancers	Thymus	Thymus
34	chr3:46599200-46600000	Enhancers	K562	blood
35	chr3:46599200-46600000	Enhancers	NHDF-Ad	bronchial
36	chr3:46599200-46600200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr3:46599200-46600200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr3:46599200-46600200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr3:46599200-46600400	Enhancers	Primary B cells from peripheral blood	blood
40	chr3:46599200-46600800	Enhancers	Fetal Heart	heart
41	chr3:46599400-46600000	Enhancers	Primary B cells from cord blood	blood
42	chr3:46599400-46600000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr3:46599400-46600000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr3:46599400-46600000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr3:46599400-46600000	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr3:46599400-46600000	Enhancers	Liver	Liver
47	chr3:46599400-46600000	Enhancers	Fetal Intestine Large	intestine
48	chr3:46599400-46600000	Enhancers	Lung	lung
49	chr3:46599400-46600000	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr3:46599400-46600000	Genic enhancers	Right Atrium	heart

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