Variant report

Variant	rs12090298
Chromosome Location	chr1:171767643-171767644
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:171750108..171754190-chr1:171766349..171769659,4	K562	blood:
2	chr1:171760261..171763188-chr1:171766979..171768595,2	MCF-7	breast:
3	chr1:171764717..171768373-chr1:171769892..171773572,7	K562	blood:
4	chr1:171749779..171754190-chr1:171762974..171767849,5	K562	blood:

Variant related genes	Relation type
ENSG00000010165	Chromatin interaction
ENSG00000213060	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10913680	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12058617	1.00[EUR][1000 genomes]
rs16843624	1.00[EUR][1000 genomes]
rs2232807	0.83[YRI][hapmap];0.82[AFR][1000 genomes]
rs41476749	1.00[EUR][1000 genomes]
rs55703533	1.00[EUR][1000 genomes]
rs55835861	1.00[EUR][1000 genomes]
rs57282067	1.00[EUR][1000 genomes]
rs57446042	1.00[EUR][1000 genomes]
rs58982503	1.00[EUR][1000 genomes]
rs59060176	1.00[EUR][1000 genomes]
rs59123048	1.00[EUR][1000 genomes]
rs59256724	1.00[EUR][1000 genomes]
rs59351676	1.00[EUR][1000 genomes]
rs59949348	1.00[EUR][1000 genomes]
rs60443600	1.00[EUR][1000 genomes]
rs60495803	1.00[EUR][1000 genomes]
rs60897561	1.00[EUR][1000 genomes]
rs61013259	1.00[EUR][1000 genomes]
rs61296253	1.00[EUR][1000 genomes]
rs61328888	1.00[EUR][1000 genomes]
rs61359014	1.00[EUR][1000 genomes]
rs6688701	1.00[EUR][1000 genomes]
rs6698195	1.00[EUR][1000 genomes]
rs6703372	1.00[EUR][1000 genomes]
rs73041915	1.00[EUR][1000 genomes]
rs73041916	1.00[EUR][1000 genomes]
rs73041963	1.00[EUR][1000 genomes]
rs73041964	1.00[EUR][1000 genomes]
rs73044063	1.00[EUR][1000 genomes]
rs74126542	1.00[EUR][1000 genomes]
rs74126543	1.00[EUR][1000 genomes]
rs74126545	1.00[EUR][1000 genomes]
rs9970108	0.94[YRI][hapmap];0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9970212	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats 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 target site	56 gene(s)	inside rSNPs	diseases
2	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv872545	chr1:171735198-171805448	Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171751600-171770800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:171752000-171773600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:171752200-171768200	Strong transcription	Fetal Muscle Trunk	muscle
4	chr1:171752600-171767800	Strong transcription	H1 Cell Line	embryonic stem cell
5	chr1:171752600-171767800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
6	chr1:171752800-171770200	Strong transcription	Rectal Mucosa Donor 29	rectum
7	chr1:171753600-171767800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:171754000-171767800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:171754000-171767800	Strong transcription	Thymus	Thymus
10	chr1:171754200-171767800	Strong transcription	Brain Anterior Caudate	brain
11	chr1:171754200-171767800	Strong transcription	Brain Germinal Matrix	brain
12	chr1:171754200-171768000	Strong transcription	Duodenum Smooth Muscle	Duodenum
13	chr1:171754200-171768000	Strong transcription	Fetal Muscle Leg	muscle
14	chr1:171754200-171769600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr1:171754200-171770200	Strong transcription	Primary T cells from cord blood	blood
16	chr1:171754200-171770200	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr1:171754400-171767800	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr1:171754400-171768200	Strong transcription	Left Ventricle	heart
19	chr1:171754600-171767800	Strong transcription	Primary hematopoietic stem cells	blood
20	chr1:171754600-171768000	Strong transcription	Liver	Liver
21	chr1:171754800-171767800	Strong transcription	Duodenum Mucosa	Duodenum
22	chr1:171754800-171768200	Strong transcription	Fetal Thymus	thymus
23	chr1:171754800-171768600	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr1:171754800-171768800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr1:171755000-171767800	Strong transcription	Gastric	stomach
26	chr1:171755000-171767800	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr1:171755000-171767800	Strong transcription	GM12878-XiMat	blood
28	chr1:171755200-171768000	Strong transcription	Esophagus	oesophagus
29	chr1:171755200-171768000	Strong transcription	Stomach Smooth Muscle	stomach
30	chr1:171755400-171767800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr1:171755400-171768000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr1:171755400-171768000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:171755400-171768200	Strong transcription	Spleen	Spleen
34	chr1:171755600-171768000	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr1:171756000-171767800	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr1:171758200-171767800	Strong transcription	Brain Cingulate Gyrus	brain
37	chr1:171758600-171768400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr1:171759200-171767800	Strong transcription	Aorta	Aorta
39	chr1:171763000-171768000	Strong transcription	Fetal Stomach	stomach
40	chr1:171763400-171768200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr1:171763800-171767800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr1:171763800-171768000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:171763800-171770400	Weak transcription	Small Intestine	intestine
44	chr1:171764000-171768000	Strong transcription	Brain Inferior Temporal Lobe	brain
45	chr1:171764000-171768200	Strong transcription	HSMM	muscle
46	chr1:171764400-171767800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr1:171764400-171767800	Strong transcription	Pancreas	Pancrea
48	chr1:171765000-171774600	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr1:171765400-171767800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr1:171765600-171768000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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