Variant report

Variant	rs549650
Chromosome Location	chr1:179888228-179888229
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179887436..179890506-chr1:179920774..179924632,4	MCF-7	breast:
2	chr1:179848878..179852546-chr1:179885763..179889262,3	K562	blood:
3	chr1:179885633..179888323-chr1:179889442..179891149,2	K562	blood:
4	chr1:179887474..179890458-chr1:179922952..179926586,3	K562	blood:
5	chr1:179887154..179888712-chr1:179922154..179924202,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143337	Chromatin interaction
ENSG00000135837	Chromatin interaction
ENSG00000260360	Chromatin interaction
ENSG00000272906	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1144575	0.93[ASN][1000 genomes]
rs1148812	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1148815	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12062341	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12062383	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1281378	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1281408	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1281411	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1281412	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1281413	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1281428	0.91[ASN][1000 genomes]
rs1281429	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1281430	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1281432	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1298477	0.81[EUR][1000 genomes]
rs1298479	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1300068	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2007148	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2245425	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2249346	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2762858	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2777908	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2777909	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2777917	0.83[AMR][1000 genomes]
rs2794582	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2794583	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs474258	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs475233	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs475434	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs479094	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs480377	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs480498	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs486906	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs501300	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs505789	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs505837	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs507603	0.90[ASN][1000 genomes]
rs514421	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs518774	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs522534	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs530369	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs530854	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs538512	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs547776	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs553830	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs555270	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs555526	0.91[ASN][1000 genomes]
rs589780	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs599185	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs600046	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs600553	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs605807	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs609521	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs612215	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs644412	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][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	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv429947	chr1:179790518-179925104	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179853000-179890400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:179853200-179890800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:179860200-179890200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr1:179867400-179897200	Weak transcription	Stomach Mucosa	stomach
5	chr1:179868200-179891600	Strong transcription	Primary B cells from peripheral blood	blood
6	chr1:179868200-179891800	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr1:179868400-179888800	Strong transcription	Adipose Nuclei	Adipose
8	chr1:179868400-179890600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:179868400-179890800	Strong transcription	Dnd41	blood
10	chr1:179868600-179891600	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr1:179868600-179892000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:179868800-179889000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr1:179868800-179889200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:179868800-179889600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr1:179869200-179891600	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr1:179869400-179889600	Strong transcription	Primary T helper cells PMA-I stimulated	--
17	chr1:179869400-179891400	Strong transcription	Liver	Liver
18	chr1:179870000-179890400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr1:179871200-179891000	Strong transcription	Duodenum Smooth Muscle	Duodenum
20	chr1:179873400-179891400	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr1:179875200-179891800	Strong transcription	Primary B cells from cord blood	blood
22	chr1:179876000-179891200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:179877000-179888600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr1:179877000-179891600	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr1:179877200-179888800	Strong transcription	Placenta	Placenta
26	chr1:179877200-179889200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:179879200-179888400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:179879600-179890800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:179880800-179891000	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr1:179881000-179891400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr1:179881200-179889400	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr1:179881400-179889600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:179881400-179889600	Strong transcription	NHDF-Ad	bronchial
34	chr1:179881600-179889000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr1:179881600-179889200	Strong transcription	Hela-S3	cervix
36	chr1:179881600-179889800	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr1:179881800-179889000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:179881800-179889000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr1:179881800-179891200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr1:179882000-179888800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr1:179882000-179888800	Strong transcription	Primary T cells from cord blood	blood
42	chr1:179882000-179889400	Strong transcription	Fetal Thymus	thymus
43	chr1:179882000-179891600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr1:179882200-179888600	Strong transcription	Fetal Intestine Large	intestine
45	chr1:179882400-179888600	Strong transcription	Stomach Smooth Muscle	stomach
46	chr1:179882400-179889000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr1:179882400-179889000	Strong transcription	Osteobl	bone
48	chr1:179882400-179889400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr1:179882600-179889800	Strong transcription	Fetal Muscle Trunk	muscle
50	chr1:179882600-179890800	Strong transcription	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links