Variant report

Variant	rs12089057
Chromosome Location	chr1:169845756-169845757
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169844705..169847129-chr1:169861263..169863239,3	MCF-7	breast:
2	chr1:169798250..169800377-chr1:169845673..169848267,2	K562	blood:
3	chr1:169844264..169846612-chr1:169869148..169870658,2	MCF-7	breast:
4	chr1:169844723..169846344-chr1:169851165..169854109,2	K562	blood:
5	chr1:169845321..169846924-chr1:169848823..169850416,2	K562	blood:
6	chr1:169845717..169848182-chr1:169860925..169862962,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000000457	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10489172	0.95[CEU][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1062976	0.95[CEU][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800468	1.00[ASN][1000 genomes]
rs10919250	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919252	0.86[CEU][hapmap];0.92[YRI][hapmap];0.85[AMR][1000 genomes]
rs10919255	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919256	0.85[AMR][1000 genomes]
rs10919258	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs10919259	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10919267	0.80[CEU][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1131498	1.00[ASN][1000 genomes]
rs11576078	0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11589247	0.86[CEU][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12059182	0.83[YRI][hapmap]
rs12064636	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12084893	1.00[ASN][1000 genomes]
rs12405525	0.85[AMR][1000 genomes]
rs12410352	0.82[AMR][1000 genomes]
rs12742961	0.83[CEU][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes]
rs12760399	0.95[CEU][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16862745	0.86[CEU][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17525350	1.00[ASN][1000 genomes]
rs17529513	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17603022	0.95[CEU][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2272918	0.83[YRI][hapmap];0.85[AMR][1000 genomes]
rs35296671	0.89[EUR][1000 genomes]
rs4987280	1.00[ASN][1000 genomes]
rs549002	0.82[AMR][1000 genomes]
rs6678351	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6694855	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73026213	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73026223	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73026243	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73026245	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	esv1814601	chr1:169782006-169885186	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv1821503	chr1:169782006-169885186	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	esv1847722	chr1:169782006-169885186	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv2757760	chr1:169782006-169885186	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv2758976	chr1:169782006-169885186	Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv428268	chr1:169782006-169885186	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1845220	chr1:169782006-169933886	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 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	chr1:169786200-169862400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:169805400-169848800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr1:169806600-169860000	Weak transcription	Stomach Mucosa	stomach
4	chr1:169814400-169848600	Strong transcription	Duodenum Mucosa	Duodenum
5	chr1:169814800-169848000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr1:169815200-169848200	Strong transcription	Primary T helper cells PMA-I stimulated	--
7	chr1:169815400-169848400	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr1:169817800-169848600	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr1:169818200-169847800	Strong transcription	Adipose Nuclei	Adipose
10	chr1:169819000-169848200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr1:169819400-169847000	Strong transcription	Liver	Liver
12	chr1:169820400-169847200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:169820600-169847800	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr1:169820600-169847800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr1:169820600-169848400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr1:169820600-169848600	Strong transcription	Fetal Lung	lung
17	chr1:169822000-169846000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
18	chr1:169825600-169845800	Strong transcription	Skeletal Muscle Female	skeletal muscle
19	chr1:169826800-169848600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr1:169831800-169848400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:169833400-169847000	Strong transcription	Left Ventricle	heart
22	chr1:169833800-169860200	Weak transcription	HMEC	breast
23	chr1:169834400-169846200	Strong transcription	HSMM	muscle
24	chr1:169837400-169848000	Strong transcription	Brain Anterior Caudate	brain
25	chr1:169840000-169846000	Strong transcription	Small Intestine	intestine
26	chr1:169840400-169846600	Strong transcription	Fetal Stomach	stomach
27	chr1:169841000-169847200	Strong transcription	Brain Substantia Nigra	brain
28	chr1:169841000-169847400	Strong transcription	Brain Inferior Temporal Lobe	brain
29	chr1:169841600-169847000	Strong transcription	Ovary	ovary
30	chr1:169841600-169847200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr1:169841800-169848200	Strong transcription	Placenta	Placenta
32	chr1:169841800-169848400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:169841800-169848400	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr1:169841800-169848600	Strong transcription	Fetal Muscle Trunk	muscle
35	chr1:169841800-169848600	Strong transcription	Fetal Muscle Leg	muscle
36	chr1:169842000-169847200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr1:169842000-169848000	Strong transcription	Thymus	Thymus
38	chr1:169842000-169848400	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr1:169842000-169848400	Strong transcription	Fetal Thymus	thymus
40	chr1:169842000-169848600	Strong transcription	Fetal Intestine Large	intestine
41	chr1:169842200-169846600	Strong transcription	Fetal Intestine Small	intestine
42	chr1:169842200-169847400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr1:169842200-169857400	Weak transcription	Fetal Brain Male	brain
44	chr1:169842400-169845800	Weak transcription	Gastric	stomach
45	chr1:169842400-169846200	Weak transcription	Aorta	Aorta
46	chr1:169842400-169847000	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr1:169842400-169847000	Weak transcription	NHLF	lung
48	chr1:169842400-169847800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr1:169842400-169848400	Strong transcription	Dnd41	blood
50	chr1:169842400-169848800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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