Variant report

Variant	rs486906
Chromosome Location	chr1:179863237-179863238
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179856725..179858627-chr1:179861974..179863939,2	K562	blood:
2	chr1:179848758..179850478-chr1:179862468..179865015,2	MCF-7	breast:
3	chr1:179849812..179857746-chr1:179862462..179868266,11	K562	blood:
4	chr1:179862982..179865680-chr1:179892718..179895012,2	MCF-7	breast:
5	chr1:179858702..179861770-chr1:179862540..179865155,3	K562	blood:

Variant related genes	Relation type
ENSG00000143337	Chromatin interaction
ENSG00000272906	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1014394	0.82[EUR][1000 genomes]
rs1148812	0.83[EUR][1000 genomes]
rs1148815	0.85[EUR][1000 genomes]
rs1148817	0.81[EUR][1000 genomes]
rs12062341	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12062383	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1281378	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1281408	0.85[EUR][1000 genomes]
rs1281411	0.85[EUR][1000 genomes]
rs1281413	0.85[EUR][1000 genomes]
rs1281429	0.84[EUR][1000 genomes]
rs1281430	0.84[EUR][1000 genomes]
rs1281432	0.85[EUR][1000 genomes]
rs1298477	0.88[EUR][1000 genomes]
rs1298479	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1300068	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2007148	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2245425	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2249346	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2762858	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2777908	0.84[EUR][1000 genomes]
rs2777909	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2794582	0.82[EUR][1000 genomes]
rs2794583	0.84[EUR][1000 genomes]
rs474258	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs475233	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs475434	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs479094	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs480377	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs480498	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs501300	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs505789	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs505837	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs514421	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs518774	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs522534	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs530369	0.81[EUR][1000 genomes]
rs530854	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs538512	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs547776	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs549650	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs553830	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs555270	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs589780	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs599185	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs600046	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs600553	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs605807	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs609521	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs612215	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs615337	0.80[EUR][1000 genomes]
rs644412	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005808	chr1:179783922-179864710	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179852800-179871200	Weak transcription	Spleen	Spleen
2	chr1:179853000-179884800	Weak transcription	Esophagus	oesophagus
3	chr1:179853000-179890400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:179853200-179886600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:179853200-179890800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:179853400-179872600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr1:179853400-179877000	Weak transcription	Right Ventricle	heart
8	chr1:179853400-179878200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:179853400-179882800	Weak transcription	Fetal Brain Male	brain
10	chr1:179854000-179865600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:179854000-179886800	Weak transcription	Fetal Heart	heart
12	chr1:179854200-179866600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:179854200-179871800	Weak transcription	Brain Germinal Matrix	brain
14	chr1:179854600-179864800	Strong transcription	Fetal Intestine Large	intestine
15	chr1:179854800-179864200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:179855200-179864600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:179855600-179871600	Weak transcription	A549	lung
18	chr1:179856000-179866000	Strong transcription	Liver	Liver
19	chr1:179856200-179876800	Weak transcription	NHLF	lung
20	chr1:179857600-179864000	Strong transcription	Dnd41	blood
21	chr1:179857600-179864800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:179857600-179864800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:179857600-179864800	Strong transcription	Adipose Nuclei	Adipose
24	chr1:179857600-179865000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr1:179857600-179866600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr1:179857600-179867400	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr1:179857600-179870000	Weak transcription	Rectal Smooth Muscle	rectum
28	chr1:179857600-179871600	Weak transcription	HSMM	muscle
29	chr1:179857600-179886800	Weak transcription	Psoas Muscle	Psoas
30	chr1:179857800-179865000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr1:179858000-179866600	Strong transcription	Primary B cells from peripheral blood	blood
32	chr1:179858200-179864800	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr1:179858200-179864800	Strong transcription	Skeletal Muscle Female	skeletal muscle
34	chr1:179858200-179865200	Strong transcription	Fetal Muscle Leg	muscle
35	chr1:179858200-179865200	Strong transcription	Stomach Smooth Muscle	stomach
36	chr1:179858200-179866000	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr1:179858200-179866000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr1:179858200-179867200	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr1:179858400-179864600	Strong transcription	Duodenum Mucosa	Duodenum
40	chr1:179858400-179864600	Strong transcription	Fetal Thymus	thymus
41	chr1:179858400-179865800	Strong transcription	Fetal Muscle Trunk	muscle
42	chr1:179858600-179864800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr1:179858600-179865400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:179858600-179865800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr1:179858600-179866000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr1:179858800-179863800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr1:179858800-179864600	Strong transcription	Colon Smooth Muscle	Colon
48	chr1:179858800-179865000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:179858800-179865800	Strong transcription	Fetal Intestine Small	intestine
50	chr1:179858800-179865800	Strong transcription	Fetal Stomach	stomach

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