Variant report

Variant	rs3750660
Chromosome Location	chr10:5987844-5987845
allele	C/T
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	FOS	chr10:5987679-5988203	MCF10A-Er-Src	breast:	n/a	chr10:5987920-5987929 chr10:5987918-5987927
2	STAT3	chr10:5987547-5988191	MCF10A-Er-Src	breast:	n/a	chr10:5987916-5987928
3	POLR2A	chr10:5987368-5988302	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr10:5986298-5988202	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr10:5987731-5988163	MCF10A-Er-Src	breast:	n/a	chr10:5987916-5987928
6	YY1	chr10:5987670-5987965	HepG2	liver:	n/a	chr10:5987925-5987944
7	POLR2A	chr10:5986317-5988310	HUVEC	blood vessel:	n/a	n/a
8	FOXP2	chr10:5987681-5988013	PFSK-1	brain:	n/a	n/a
9	MYC	chr10:5987690-5988103	HUVEC	blood vessel:	n/a	chr10:5987921-5987931
10	CEBPB	chr10:5987745-5988318	HepG2	liver:	n/a	chr10:5987884-5987895 chr10:5987882-5987893 chr10:5987882-5987895
11	MYC	chr10:5987449-5988285	MCF10A-Er-Src	breast:	n/a	chr10:5987921-5987931
12	CTCF	chr10:5987800-5987950	HAc	cerebellar:	n/a	n/a
13	MYC	chr10:5987650-5988149	NB4	blood:	n/a	chr10:5987921-5987931
14	GABPA	chr10:5987769-5987916	HepG2	liver:	n/a	n/a
15	FOS	chr10:5987782-5988154	MCF10A-Er-Src	breast:	n/a	chr10:5987920-5987929 chr10:5987918-5987927
16	MYC	chr10:5987501-5988162	MCF10A-Er-Src	breast:	n/a	chr10:5987921-5987931
17	STAT3	chr10:5986331-5988300	MCF10A-Er-Src	breast:	n/a	chr10:5987916-5987928 chr10:5987265-5987273
18	POLR2A	chr10:5987362-5988508	HUVEC	blood vessel:	n/a	n/a
19	CEBPB	chr10:5987788-5987992	K562	blood:	n/a	chr10:5987884-5987895 chr10:5987882-5987893 chr10:5987882-5987895
20	CEBPB	chr10:5987709-5988062	H1-hESC	embryonic stem cell:	n/a	chr10:5987884-5987895 chr10:5987882-5987893 chr10:5987882-5987895
21	GATA2	chr10:5987206-5988301	HUVEC	blood vessel:	n/a	n/a
22	POLR2A	chr10:5987330-5988364	HUVEC	blood vessel:	n/a	n/a
23	CEBPB	chr10:5987526-5988456	IMR90	lung:	n/a	chr10:5987884-5987895 chr10:5987882-5987893 chr10:5987882-5987895
24	POLR2A	chr10:5985575-5988373	IMR90	lung:	n/a	n/a
25	POLR2A	chr10:5985398-5988391	HUVEC	blood vessel:	n/a	n/a
26	MAX	chr10:5987715-5988072	NB4	blood:	n/a	chr10:5987921-5987931
27	POLR2A	chr10:5986303-5988221	MCF10A-Er-Src	breast:	n/a	n/a
28	E2F4	chr10:5987829-5988140	MCF10A-Er-Src	breast:	n/a	n/a
29	FOS	chr10:5987600-5988276	HUVEC	blood vessel:	n/a	chr10:5987920-5987929 chr10:5987918-5987927
30	POLR2A	chr10:5987620-5988234	HUVEC	blood vessel:	n/a	n/a
31	FOXP2	chr10:5987707-5988083	PFSK-1	brain:	n/a	n/a
32	CEBPB	chr10:5987800-5987936	HepG2	liver:	n/a	chr10:5987884-5987895 chr10:5987882-5987893 chr10:5987882-5987895
33	STAT3	chr10:5987754-5987954	MCF10A-Er-Src	breast:	n/a	chr10:5987916-5987928

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:5958041..5960183-chr10:5985968..5987908,2	K562	blood:
2	chr10:5987354..5989797-chr10:6018047..6020538,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IL15RA-1	chr10:5987618-5987863	ENSG00000232807.1

Variant related genes	Relation type
ENSG00000232807	TF binding region
ENSG00000134452	Chromatin interaction
ENSG00000134470	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11256083	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11256084	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11256085	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11256090	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11256094	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11256096	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12242015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12242172	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12245981	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12248076	0.96[ASN][1000 genomes]
rs12250688	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12258180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs28686883	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3136628	0.93[ASN][1000 genomes]
rs3136629	0.93[ASN][1000 genomes]
rs41293979	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41293999	0.96[ASN][1000 genomes]
rs41294001	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41294003	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41294005	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41294007	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41294017	1.00[AMR][1000 genomes]
rs41294025	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41294027	0.96[ASN][1000 genomes]
rs41294039	0.93[ASN][1000 genomes]
rs7923984	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8177726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[ASN][1000 genomes]
rs8177732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs8177741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[ASN][1000 genomes]
rs8177742	0.93[ASN][1000 genomes]
rs8177772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs8177775	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs8177776	0.81[ASN][1000 genomes]
rs8177778	0.90[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:110 , 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	chr10:5978800-5988200	Weak transcription	Fetal Brain Male	brain
4	chr10:5980000-5991000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr10:5980000-6013200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr10:5980800-5991000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr10:5980800-5994600	Weak transcription	Gastric	stomach
8	chr10:5980800-6017800	Weak transcription	Thymus	Thymus
9	chr10:5981000-5988000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr10:5981000-6003600	Weak transcription	Primary T cells from cord blood	blood
11	chr10:5982800-5995000	Weak transcription	GM12878-XiMat	blood
12	chr10:5983400-5989000	Enhancers	Fetal Stomach	stomach
13	chr10:5983600-5988600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr10:5984600-5989000	Enhancers	Fetal Muscle Trunk	muscle
15	chr10:5985200-5989200	Enhancers	Spleen	Spleen
16	chr10:5985400-5988400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr10:5985400-5988400	Enhancers	Fetal Kidney	kidney
18	chr10:5985400-5988600	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr10:5985600-5988200	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr10:5985600-5990000	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr10:5986000-5988400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr10:5986200-5988400	Flanking Active TSS	HUVEC	blood vessel
23	chr10:5986200-5989000	Enhancers	Brain Substantia Nigra	brain
24	chr10:5986200-5991400	Weak transcription	Right Ventricle	heart
25	chr10:5986200-6018600	Weak transcription	Aorta	Aorta
26	chr10:5986400-5988000	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr10:5986400-5988200	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr10:5986400-5988400	Flanking Active TSS	Colon Smooth Muscle	Colon
29	chr10:5986600-5988200	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr10:5986600-5988200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
31	chr10:5986600-5988200	Flanking Active TSS	HSMMtube	muscle
32	chr10:5986600-5988400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr10:5986600-5988400	Flanking Active TSS	NHDF-Ad	bronchial
34	chr10:5986600-5988400	Flanking Active TSS	NHLF	lung
35	chr10:5986600-5988400	Flanking Active TSS	Osteobl	bone
36	chr10:5986800-5988400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
37	chr10:5986800-5988400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr10:5986800-5988400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr10:5986800-5988400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr10:5986800-5988400	Enhancers	Hela-S3	cervix
41	chr10:5986800-5989200	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr10:5986800-5989400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr10:5986800-5995600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr10:5987000-5988000	Flanking Active TSS	Placenta	Placenta
45	chr10:5987000-5988000	Flanking Active TSS	Ovary	ovary
46	chr10:5987000-5988200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
47	chr10:5987000-5988400	Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr10:5987000-5994600	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr10:5987200-5988000	Active TSS	Colonic Mucosa	Colon
50	chr10:5987200-5988200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast

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