Variant report

Variant	rs2280408
Chromosome Location	chr3:46599457-46599458
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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	chr3:46529686..46530942-chr3:46599020..46600485,46	MCF-7	breast:
4	chr3:46498573..46499197-chr3:46599063..46599998,2	K562	blood:
5	chr3:46529889..46530997-chr3:46599244..46600312,18	MCF-7	breast:
6	chr3:46599422..46601505-chr3:46601570..46603414,2	K562	blood:

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs17286758	0.81[CHB][hapmap]
rs2280409	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280410	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]
rs2280413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[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];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2293021	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2293022	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2293023	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2293024	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2293025	1.00[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	1.00[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3827493	1.00[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];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55649212	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55693118	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55736632	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55763532	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55923987	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55955974	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55957516	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56008703	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56048308	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56163098	0.84[AMR][1000 genomes]
rs56168669	0.84[AMR][1000 genomes]
rs56188400	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56197743	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56394040	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56398705	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56695799	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58177689	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58551379	0.84[AMR][1000 genomes]
rs58572135	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59673973	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59836693	1.00[AFR][1000 genomes];1.00[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]
rs6783443	0.81[CHB][hapmap]
rs73069984	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73069987	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73069989	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73069992	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73069996	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73069997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73071917	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73071919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73071930	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73071938	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73072002	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73073704	0.81[ASN][1000 genomes]
rs73073732	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73073734	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73073742	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73073744	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73073745	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73073746	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73073750	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73073752	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73073753	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73073754	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73073755	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73075515	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73075519	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73075524	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73075528	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73075540	0.83[AMR][1000 genomes]
rs73075543	0.83[AMR][1000 genomes]
rs73075564	0.96[AMR][1000 genomes]
rs73075571	0.96[AMR][1000 genomes]
rs73077539	0.84[AMR][1000 genomes]
rs73077544	0.84[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:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46587800-46599600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr3:46588400-46599600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr3:46591000-46599600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr3:46591400-46600200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:46591600-46599800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr3:46591600-46600000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr3:46591800-46606600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:46593000-46600200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:46593200-46600000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:46593200-46600000	Weak transcription	Ovary	ovary
11	chr3:46597000-46600000	Enhancers	HUVEC	blood vessel
12	chr3:46597800-46600000	Enhancers	Muscle Satellite Cultured Cells	--
13	chr3:46597800-46600000	Enhancers	Hela-S3	cervix
14	chr3:46598000-46599600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:46598000-46599800	Enhancers	NHEK	skin
16	chr3:46598400-46599800	Enhancers	HMEC	breast
17	chr3:46598400-46600000	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr3:46598400-46600000	Enhancers	HSMM	muscle
19	chr3:46598400-46600200	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr3:46598400-46601000	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr3:46598600-46599600	Enhancers	Osteobl	bone
22	chr3:46598600-46599800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:46598600-46600000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr3:46598600-46600000	Enhancers	NH-A	brain
25	chr3:46598800-46599600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr3:46598800-46599800	Enhancers	H9 Cell Line	embryonic stem cell
27	chr3:46598800-46600000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr3:46598800-46600000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:46598800-46600000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr3:46598800-46600000	Enhancers	NHLF	lung
31	chr3:46598800-46600400	Enhancers	H1 Cell Line	embryonic stem cell
32	chr3:46599000-46600000	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr3:46599000-46600200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr3:46599000-46600400	Enhancers	Dnd41	blood
35	chr3:46599000-46601200	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr3:46599200-46599600	Genic enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr3:46599200-46599600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr3:46599200-46599600	Enhancers	Duodenum Mucosa	Duodenum
39	chr3:46599200-46599600	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr3:46599200-46599800	Enhancers	Primary T cells from cord blood	blood
41	chr3:46599200-46599800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
42	chr3:46599200-46600000	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr3:46599200-46600000	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr3:46599200-46600000	Enhancers	Fetal Thymus	thymus
45	chr3:46599200-46600000	Enhancers	Gastric	stomach
46	chr3:46599200-46600000	Enhancers	Left Ventricle	heart
47	chr3:46599200-46600000	Enhancers	Pancreas	Pancrea
48	chr3:46599200-46600000	Enhancers	Psoas Muscle	Psoas
49	chr3:46599200-46600000	Enhancers	Right Ventricle	heart
50	chr3:46599200-46600000	Enhancers	Thymus	Thymus

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