Variant report

Variant	rs13374592
Chromosome Location	chr1:184372203-184372204
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:184355543..184357815-chr1:184370746..184372746,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271387	Chromatin interaction
ENSG00000116667	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10911585	0.89[EUR][1000 genomes]
rs10911586	0.89[EUR][1000 genomes]
rs10911597	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11799574	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs12116705	0.92[EUR][1000 genomes]
rs12123538	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs12128343	1.00[CEU][hapmap];0.90[AMR][1000 genomes]
rs12128424	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12129504	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12130008	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12131730	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12132220	0.92[EUR][1000 genomes]
rs12136470	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12138263	0.90[AMR][1000 genomes]
rs12140904	0.90[EUR][1000 genomes]
rs12142338	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12142568	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs12142676	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12145326	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs12354368	0.92[EUR][1000 genomes]
rs16823133	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17576899	0.92[EUR][1000 genomes]
rs17577247	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs56173711	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59688287	0.82[AFR][1000 genomes]
rs60650088	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74131663	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs74131672	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs74131673	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7531736	0.85[GIH][hapmap]
rs9803754	0.85[EUR][1000 genomes]
rs9804057	0.85[EUR][1000 genomes]
rs9970469	1.00[CEU][hapmap];0.92[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530079	chr1:183797938-184639971	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184358000-184373400	Weak transcription	Ovary	ovary
2	chr1:184358200-184374000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:184358400-184378200	Weak transcription	Brain Angular Gyrus	brain
4	chr1:184359000-184382800	Weak transcription	Fetal Stomach	stomach
5	chr1:184359400-184377000	Weak transcription	Fetal Intestine Small	intestine
6	chr1:184359600-184377000	Weak transcription	A549	lung
7	chr1:184359600-184391200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr1:184360600-184386200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr1:184362400-184374800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr1:184362600-184374000	Weak transcription	Esophagus	oesophagus
11	chr1:184362600-184374400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:184362600-184377000	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr1:184362600-184386200	Weak transcription	Lung	lung
14	chr1:184362800-184374200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr1:184364800-184373600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:184365000-184378200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:184365200-184376800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:184365600-184373400	Weak transcription	Small Intestine	intestine
19	chr1:184367600-184373200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr1:184368400-184373800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:184368800-184373600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:184369000-184375800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr1:184369000-184377000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:184369000-184377200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr1:184369200-184376800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr1:184369200-184377400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr1:184370200-184373200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr1:184371200-184372400	Enhancers	Psoas Muscle	Psoas
29	chr1:184371400-184372400	Enhancers	Fetal Heart	heart
30	chr1:184371400-184372400	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr1:184371400-184372600	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr1:184371800-184372400	Enhancers	Stomach Smooth Muscle	stomach
33	chr1:184371800-184372600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:184371800-184378400	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr1:184372000-184372400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:184372000-184373800	Weak transcription	Brain Germinal Matrix	brain
37	chr1:184372000-184374400	Weak transcription	Left Ventricle	heart
38	chr1:184372000-184375200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr1:184372200-184372800	Enhancers	Fetal Kidney	kidney
40	chr1:184372200-184373800	Weak transcription	Adipose Nuclei	Adipose
41	chr1:184372200-184373800	Weak transcription	Fetal Lung	lung
42	chr1:184372200-184375200	Weak transcription	Colon Smooth Muscle	Colon
43	chr1:184372200-184376200	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr1:184372200-184377000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:184372200-184377800	Weak transcription	Right Atrium	heart
46	chr1:184372200-184382800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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