Variant report

Variant	rs28686883
Chromosome Location	chr10:5988427-5988428
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:5987362-5988508	HUVEC	blood vessel:	n/a	n/a
2	CEBPB	chr10:5987526-5988456	IMR90	lung:	n/a	chr10:5987884-5987895 chr10:5987882-5987893 chr10:5987882-5987895

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:5987354..5989797-chr10:6018047..6020538,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232807	TF binding region
ENSG00000134470	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11256083	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11256084	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11256085	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11256090	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11256094	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11256096	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12242015	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12242172	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12245981	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12248076	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12250688	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12258180	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3136628	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3136629	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3750660	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41293979	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41293999	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41294001	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41294003	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41294005	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41294007	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41294017	0.82[EUR][1000 genomes]
rs41294025	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41294027	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41294039	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7923984	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8177726	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8177732	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8177741	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8177742	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8177778	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34147	chr10:5726821-6105717	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv34061	chr10:5726821-6225187	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv831775	chr10:5804335-6000849	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1041261	chr10:5962635-6052196	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1050983	chr10:5963921-6052196	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5969600-6012000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr10:5971400-6013200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr10:5980000-5991000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr10:5980000-6013200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr10:5980800-5991000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr10:5980800-5994600	Weak transcription	Gastric	stomach
7	chr10:5980800-6017800	Weak transcription	Thymus	Thymus
8	chr10:5981000-6003600	Weak transcription	Primary T cells from cord blood	blood
9	chr10:5982800-5995000	Weak transcription	GM12878-XiMat	blood
10	chr10:5983400-5989000	Enhancers	Fetal Stomach	stomach
11	chr10:5983600-5988600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr10:5984600-5989000	Enhancers	Fetal Muscle Trunk	muscle
13	chr10:5985200-5989200	Enhancers	Spleen	Spleen
14	chr10:5985400-5988600	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr10:5985600-5990000	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr10:5986200-5989000	Enhancers	Brain Substantia Nigra	brain
17	chr10:5986200-5991400	Weak transcription	Right Ventricle	heart
18	chr10:5986200-6018600	Weak transcription	Aorta	Aorta
19	chr10:5986800-5989200	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr10:5986800-5989400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr10:5986800-5995600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr10:5987000-5994600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr10:5987200-5988600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr10:5987200-5991000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr10:5987200-5991000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr10:5987200-5991000	Weak transcription	Fetal Intestine Small	intestine
27	chr10:5987400-5989200	Enhancers	H9 Cell Line	embryonic stem cell
28	chr10:5987600-5989000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr10:5987600-5991000	Weak transcription	Pancreas	Pancrea
30	chr10:5987600-5991000	Weak transcription	A549	lung
31	chr10:5987600-5992400	Weak transcription	Brain Angular Gyrus	brain
32	chr10:5987600-6018000	Weak transcription	Psoas Muscle	Psoas
33	chr10:5987800-5989200	Enhancers	Brain Anterior Caudate	brain
34	chr10:5987800-5989200	Enhancers	Left Ventricle	heart
35	chr10:5987800-5989200	Enhancers	Lung	lung
36	chr10:5987800-5989200	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr10:5987800-5989200	Weak transcription	K562	blood
38	chr10:5987800-5989400	Enhancers	Fetal Muscle Leg	muscle
39	chr10:5987800-5992400	Weak transcription	Esophagus	oesophagus
40	chr10:5987800-5993600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr10:5987800-6017800	Weak transcription	Fetal Thymus	thymus
42	chr10:5988000-5988600	Enhancers	HMEC	breast
43	chr10:5988000-5989400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
44	chr10:5988000-5989400	Enhancers	Placenta	Placenta
45	chr10:5988000-5994000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr10:5988000-5995000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr10:5988000-6000800	Weak transcription	Colonic Mucosa	Colon
48	chr10:5988000-6001400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr10:5988200-5988600	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr10:5988200-5988600	Enhancers	Muscle Satellite Cultured Cells	--

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