Variant report

Variant	rs12080691
Chromosome Location	chr1:210007416-210007417
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:210006373..210009984-chr1:210010286..210013558,6	K562	blood:
2	chr1:210005828..210008721-chr1:210008768..210010506,3	MCF-7	breast:
3	chr1:210001362..210003899-chr1:210005802..210009709,4	K562	blood:

Variant related genes	Relation type
ENSG00000117597	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10489343	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10779514	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10779515	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10863789	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10863790	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1109430	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11119345	0.87[AMR][1000 genomes]
rs11119346	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11119347	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11119348	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12058100	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs12062600	0.81[AMR][1000 genomes]
rs12063989	0.81[AMR][1000 genomes]
rs12064085	0.81[AMR][1000 genomes]
rs12064211	0.81[AMR][1000 genomes]
rs12064398	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12069187	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12075674	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12078157	0.81[AMR][1000 genomes]
rs12081405	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12083685	1.00[CEU][hapmap]
rs12405750	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12563527	0.81[AMR][1000 genomes]
rs12566152	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17015217	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17015255	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17015268	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1856161	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1883332	0.81[AMR][1000 genomes]
rs2069068	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2235370	0.81[AMR][1000 genomes]
rs2235371	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2235377	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3753517	0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41274836	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4140636	1.00[CEU][hapmap]
rs4329516	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4844494	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4844496	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4844908	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210001800-210010200	Weak transcription	Spleen	Spleen
2	chr1:210001800-210025000	Weak transcription	Stomach Mucosa	stomach
3	chr1:210001800-210034000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:210002000-210011200	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr1:210002000-210015600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:210002000-210023800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:210002400-210032000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:210003000-210009800	Weak transcription	Small Intestine	intestine
9	chr1:210003000-210011000	Weak transcription	Fetal Heart	heart
10	chr1:210003000-210013200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:210003200-210007600	Weak transcription	Psoas Muscle	Psoas
12	chr1:210003200-210017400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:210003200-210027800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:210003200-210028600	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr1:210003200-210029400	Strong transcription	Fetal Muscle Trunk	muscle
16	chr1:210003400-210028000	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr1:210003400-210028400	Strong transcription	Primary B cells from peripheral blood	blood
18	chr1:210003600-210012200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:210003600-210028000	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr1:210003800-210011800	Strong transcription	A549	lung
21	chr1:210003800-210013200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr1:210003800-210028000	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr1:210003800-210028200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr1:210003800-210028400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:210004000-210012000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:210004000-210015800	Genic enhancers	NHDF-Ad	bronchial
27	chr1:210004000-210019000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
28	chr1:210004000-210019000	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr1:210004000-210021400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr1:210004000-210027600	Strong transcription	K562	blood
31	chr1:210004000-210027800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:210004000-210028000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr1:210004000-210028000	Strong transcription	Fetal Thymus	thymus
34	chr1:210004000-210028200	Strong transcription	Duodenum Mucosa	Duodenum
35	chr1:210004000-210030800	Strong transcription	Primary B cells from cord blood	blood
36	chr1:210004200-210008800	Strong transcription	HepG2	liver
37	chr1:210004200-210009000	Strong transcription	Colon Smooth Muscle	Colon
38	chr1:210004200-210009000	Strong transcription	Fetal Kidney	kidney
39	chr1:210004200-210009200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr1:210004200-210010800	Strong transcription	Liver	Liver
41	chr1:210004200-210011400	Strong transcription	Fetal Intestine Large	intestine
42	chr1:210004200-210013000	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr1:210004200-210013200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr1:210004200-210013200	Strong transcription	Skeletal Muscle Male	skeletal muscle
45	chr1:210004200-210017600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:210004200-210018200	Strong transcription	Brain Substantia Nigra	brain
47	chr1:210004200-210018600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
48	chr1:210004200-210018600	Strong transcription	Fetal Lung	lung
49	chr1:210004200-210018600	Strong transcription	Left Ventricle	heart
50	chr1:210004200-210018800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links