Variant report

Variant	rs12409923
Chromosome Location	chr1:180448029-180448030
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:180446739..180449088-chr1:180449481..180452200,3	MCF-7	breast:
2	chr1:180447230..180448996-chr1:180450484..180453034,2	K562	blood:
3	chr1:180445158..180449486-chr1:180469898..180473784,7	MCF-7	breast:
4	chr1:180442608..180444717-chr1:180447768..180449648,2	K562	blood:
5	chr1:180425851..180427880-chr1:180446701..180449682,2	K562	blood:
6	chr1:180446432..180448088-chr1:180465802..180468652,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135847	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10494526	1.00[AFR][1000 genomes]
rs10913960	1.00[AFR][1000 genomes]
rs10913963	0.81[ASN][1000 genomes]
rs10913975	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10913977	0.94[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12037744	0.87[ASN][1000 genomes]
rs12089448	0.84[ASN][1000 genomes]
rs12403226	1.00[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12404700	0.80[ASN][1000 genomes]
rs2025593	0.87[ASN][1000 genomes]
rs2877481	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs36088499	1.00[AFR][1000 genomes]
rs6425646	0.81[ASN][1000 genomes]
rs6684596	0.89[ASN][1000 genomes]
rs878641	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003739	chr1:180027760-180483292	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv535217	chr1:180027760-180483292	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv1013716	chr1:180287338-180477072	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
4	nsv535221	chr1:180287338-180477072	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
5	esv2762200	chr1:180300936-180493841	ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
6	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
7	nsv949311	chr1:180438895-180692815	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180404400-180469000	Weak transcription	Pancreas	Pancrea
2	chr1:180421200-180451600	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr1:180425800-180457600	Weak transcription	Aorta	Aorta
4	chr1:180427400-180448200	Weak transcription	Osteobl	bone
5	chr1:180428000-180470000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr1:180429600-180455000	Weak transcription	Left Ventricle	heart
7	chr1:180430200-180454600	Weak transcription	Thymus	Thymus
8	chr1:180431200-180470200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:180431400-180448200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:180432000-180451400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr1:180432000-180470600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:180433600-180454200	Weak transcription	Adipose Nuclei	Adipose
13	chr1:180433800-180455000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr1:180434000-180465600	Weak transcription	Fetal Brain Male	brain
15	chr1:180434200-180470200	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr1:180434400-180451400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr1:180434600-180448200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:180434600-180448200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:180434600-180448400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr1:180434800-180451400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr1:180434800-180458800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr1:180435000-180456400	Weak transcription	Fetal Kidney	kidney
23	chr1:180435200-180454400	Weak transcription	Fetal Muscle Trunk	muscle
24	chr1:180435200-180469000	Weak transcription	Brain Angular Gyrus	brain
25	chr1:180435400-180448200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr1:180435600-180448600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr1:180436600-180450400	Weak transcription	NHDF-Ad	bronchial
28	chr1:180437600-180448800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:180437600-180451400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr1:180437600-180454600	Weak transcription	Gastric	stomach
31	chr1:180437600-180455200	Weak transcription	Ovary	ovary
32	chr1:180437600-180470400	Weak transcription	Right Ventricle	heart
33	chr1:180437600-180470600	Weak transcription	Spleen	Spleen
34	chr1:180437600-180471000	Weak transcription	Lung	lung
35	chr1:180437800-180454400	Weak transcription	Fetal Intestine Large	intestine
36	chr1:180438200-180451400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr1:180438400-180453000	Weak transcription	Placenta	Placenta
38	chr1:180438600-180448400	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr1:180438600-180451400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr1:180438600-180454400	Weak transcription	Fetal Thymus	thymus
41	chr1:180438800-180451400	Weak transcription	HUVEC	blood vessel
42	chr1:180438800-180454400	Weak transcription	HepG2	liver
43	chr1:180439200-180448600	Weak transcription	NHEK	skin
44	chr1:180439800-180448200	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr1:180440000-180448200	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr1:180440000-180451800	Weak transcription	Brain Hippocampus Middle	brain
47	chr1:180440000-180455200	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr1:180440000-180469000	Weak transcription	HSMMtube	muscle
49	chr1:180440200-180468400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr1:180440200-180469000	Weak transcription	Skeletal Muscle Male	skeletal muscle

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