Variant report

Variant	rs480549
Chromosome Location	chr15:41406942-41406943
allele	C/G
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:41404323..41407208-chr15:41574690..41577351,2	K562	blood:
2	chr15:41406758..41409601-chr15:41707795..41710639,2	MCF-7	breast:
3	chr15:41406937..41409542-chr15:41521164..41524731,5	K562	blood:
4	chr15:41406745..41409392-chr15:41623521..41626579,5	K562	blood:
5	chr15:41056057..41058777-chr15:41406413..41409021,2	K562	blood:
6	chr15:40875804..40877878-chr15:41405943..41408049,2	K562	blood:
7	chr15:41406809..41409126-chr15:41623521..41625356,3	K562	blood:
8	chr15:41396638..41398634-chr15:41406036..41407580,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000137804	Chromatin interaction
ENSG00000247556	Chromatin interaction
ENSG00000137880	Chromatin interaction
ENSG00000187446	Chromatin interaction
ENSG00000104147	Chromatin interaction
ENSG00000137815	Chromatin interaction
ENSG00000178997	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10152296	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11070319	0.94[AMR][1000 genomes]
rs11070320	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11630905	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs16971263	0.83[AMR][1000 genomes]
rs16971463	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2007255	0.84[AMR][1000 genomes]
rs2412599	1.00[EUR][1000 genomes]
rs2412600	1.00[EUR][1000 genomes]
rs28455970	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28528813	0.89[AMR][1000 genomes]
rs2899010	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2925348	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs2925349	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2927067	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2928147	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2928149	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2928150	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2928154	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2947492	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs2947495	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2947496	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs2955812	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3101435	0.83[AMR][1000 genomes]
rs3101438	1.00[AMR][1000 genomes]
rs3101441	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs4468583	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs474351	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs487779	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4923894	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4923895	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs4924533	0.84[AMR][1000 genomes]
rs4924534	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs496499	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs513680	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs518137	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs525551	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs538903	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs56955512	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57008457	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs57385441	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58142514	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs59405359	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs690773	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs691069	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs691722	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs692703	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs7162003	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs7167166	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7172555	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7173146	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7174223	1.00[EUR][1000 genomes]
rs7174513	1.00[AMR][1000 genomes]
rs7183191	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs73399092	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8032956	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8034461	0.94[AMR][1000 genomes]
rs8035532	1.00[AMR][1000 genomes]
rs8043232	0.89[AMR][1000 genomes]
rs9806344	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569229	chr15:41361138-41483682	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv904107	chr15:41361138-41493013	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv569230	chr15:41384649-41483682	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv904108	chr15:41384649-41486990	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41361200-41407200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:41383800-41407400	Weak transcription	Esophagus	oesophagus
3	chr15:41384000-41407400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr15:41384400-41407400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr15:41386200-41407400	Weak transcription	Aorta	Aorta
6	chr15:41386600-41407400	Weak transcription	Colonic Mucosa	Colon
7	chr15:41386800-41407000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr15:41386800-41407200	Weak transcription	HSMMtube	muscle
9	chr15:41386800-41407400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr15:41387400-41407200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr15:41388600-41407000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr15:41388600-41407000	Weak transcription	Fetal Kidney	kidney
13	chr15:41388600-41407200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr15:41388600-41407200	Weak transcription	Brain Anterior Caudate	brain
15	chr15:41388600-41407400	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr15:41388800-41407000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr15:41388800-41407000	Weak transcription	Fetal Intestine Large	intestine
18	chr15:41391000-41407400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr15:41391600-41407000	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr15:41395600-41407200	Weak transcription	HSMM	muscle
21	chr15:41396000-41407000	Weak transcription	NHDF-Ad	bronchial
22	chr15:41398600-41407200	Weak transcription	Small Intestine	intestine
23	chr15:41398800-41407000	Weak transcription	Brain Angular Gyrus	brain
24	chr15:41398800-41407000	Weak transcription	NHLF	lung
25	chr15:41398800-41407200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr15:41398800-41407200	Weak transcription	Left Ventricle	heart
27	chr15:41398800-41407400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr15:41398800-41407400	Weak transcription	Lung	lung
29	chr15:41400600-41407400	Weak transcription	Gastric	stomach
30	chr15:41401200-41407000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr15:41401200-41407000	Weak transcription	Duodenum Mucosa	Duodenum
32	chr15:41401200-41407000	Weak transcription	NHEK	skin
33	chr15:41401200-41407200	Weak transcription	Brain Germinal Matrix	brain
34	chr15:41401400-41407000	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr15:41401600-41407000	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr15:41401800-41407000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr15:41401800-41407000	Weak transcription	Primary T cells from cord blood	blood
38	chr15:41402800-41407200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr15:41402800-41407200	Weak transcription	Thymus	Thymus
40	chr15:41403400-41407000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr15:41403400-41407000	Strong transcription	Fetal Stomach	stomach
42	chr15:41404600-41407000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr15:41404600-41407000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr15:41405400-41407600	Enhancers	Spleen	Spleen
45	chr15:41405600-41407200	Enhancers	Primary T cells fromperipheralblood	blood
46	chr15:41405800-41407000	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr15:41405800-41407200	Enhancers	Primary T helper cells fromperipheralblood	blood
48	chr15:41406000-41407000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
49	chr15:41406000-41407000	Enhancers	Brain Hippocampus Middle	brain
50	chr15:41406000-41407000	Enhancers	HepG2	liver

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