Variant report

Variant	rs28549326
Chromosome Location	chr15:39918243-39918244
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:39887137..39895767-chr15:39912868..39924962,20	MCF-7	breast:
2	chr15:39913171..39923947-chr15:39954798..39966806,32	MCF-7	breast:

Variant related genes	Relation type
ENSG00000150667	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1038097	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1051442	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10520141	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10520143	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10520146	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10520148	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1382443	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1382444	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16969487	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16969491	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16969547	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17632916	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17633107	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17633210	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17705806	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17706083	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17706179	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1813493	0.91[EUR][1000 genomes]
rs1988082	0.82[EUR][1000 genomes]
rs1988555	0.85[EUR][1000 genomes]
rs1994380	0.80[EUR][1000 genomes]
rs2129457	0.80[EUR][1000 genomes]
rs2228263	0.94[EUR][1000 genomes]
rs2411316	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2618156	0.91[EUR][1000 genomes]
rs2618160	0.91[EUR][1000 genomes]
rs2618161	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2618164	0.91[EUR][1000 genomes]
rs2618165	0.91[EUR][1000 genomes]
rs2618167	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2664123	0.91[EUR][1000 genomes]
rs2664136	0.91[EUR][1000 genomes]
rs2664137	0.91[EUR][1000 genomes]
rs2664138	0.90[EUR][1000 genomes]
rs2664140	0.91[EUR][1000 genomes]
rs2664142	0.91[EUR][1000 genomes]
rs28377784	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28619289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28653011	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34878675	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4085744	0.80[AMR][1000 genomes]
rs41315060	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4415979	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4503768	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs45461294	0.95[EUR][1000 genomes]
rs4923835	0.85[EUR][1000 genomes]
rs58188999	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59578395	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59628570	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6492905	0.94[EUR][1000 genomes]
rs74008647	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs74008648	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs880270	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs954152	0.92[EUR][1000 genomes]
rs9972350	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv904094	chr15:39738006-39976057	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv832977	chr15:39817512-39981520	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1048628	chr15:39877498-39940104	Enhancers Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1502	chr15:39884314-39928968	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
8	nsv832978	chr15:39899759-40094881	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39913200-39924000	Enhancers	Rectal Mucosa Donor 31	rectum
2	chr15:39913400-39921000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr15:39913400-39922400	Enhancers	Fetal Intestine Large	intestine
4	chr15:39913400-39923800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr15:39914000-39922800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr15:39914200-39922600	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr15:39914600-39922800	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr15:39914600-39923600	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr15:39914600-39923600	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr15:39914600-39923800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr15:39914800-39923800	Enhancers	Primary T cells fromperipheralblood	blood
12	chr15:39915200-39918400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr15:39915400-39918800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
14	chr15:39915800-39918800	Enhancers	HUVEC	blood vessel
15	chr15:39916000-39918600	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr15:39916000-39918800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr15:39916000-39920000	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr15:39916000-39922200	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr15:39916000-39924000	Enhancers	HMEC	breast
20	chr15:39916200-39918600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr15:39916200-39918800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr15:39916200-39920800	Enhancers	Spleen	Spleen
23	chr15:39916200-39921000	Weak transcription	Thymus	Thymus
24	chr15:39916200-39922200	Enhancers	Left Ventricle	heart
25	chr15:39916200-39923400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr15:39916400-39918400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr15:39916400-39918600	Enhancers	NHEK	skin
28	chr15:39916400-39918600	Enhancers	NHLF	lung
29	chr15:39916400-39937800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr15:39916600-39918400	Enhancers	NH-A	brain
31	chr15:39916600-39918400	Enhancers	Osteobl	bone
32	chr15:39916600-39918600	Enhancers	Muscle Satellite Cultured Cells	--
33	chr15:39916600-39918600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr15:39916600-39918600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr15:39916600-39918600	Enhancers	Hela-S3	cervix
36	chr15:39916600-39918800	Enhancers	NHDF-Ad	bronchial
37	chr15:39916600-39919600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr15:39916600-39921000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr15:39916800-39921600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
40	chr15:39916800-39921800	Enhancers	Right Ventricle	heart
41	chr15:39917000-39920400	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr15:39917400-39918400	Enhancers	GM12878-XiMat	blood
43	chr15:39917400-39923800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr15:39917600-39918600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr15:39917600-39919800	Enhancers	Fetal Heart	heart
46	chr15:39917600-39920200	Weak transcription	Aorta	Aorta
47	chr15:39917600-39920400	Weak transcription	Psoas Muscle	Psoas
48	chr15:39917600-39920800	Weak transcription	Colon Smooth Muscle	Colon
49	chr15:39917600-39921000	Weak transcription	Primary hematopoietic stem cells	blood
50	chr15:39917600-39921600	Weak transcription	Monocytes-CD14+_RO01746	blood

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