Variant report

Variant	rs2251618
Chromosome Location	chr12:26181685-26181686
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	chr12:26110820..26113756-chr12:26181378..26183569,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000246695	Chromatin interaction
ENSG00000123094	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10431215	0.85[ASN][1000 genomes]
rs10459081	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs10771250	0.85[CHB][hapmap];0.95[GIH][hapmap]
rs10771251	0.81[MEX][hapmap]
rs10771253	0.80[MEX][hapmap]
rs10771255	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10842651	0.89[CHB][hapmap];0.87[JPT][hapmap];0.84[YRI][hapmap];0.81[ASN][1000 genomes]
rs10842655	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10842658	0.89[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10842659	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11048363	0.85[CHB][hapmap]
rs11048370	0.81[ASN][1000 genomes]
rs11048374	0.87[ASN][1000 genomes]
rs12369462	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1513124	0.89[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1874351	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1986802	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1994995	0.94[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.82[MEX][hapmap];0.85[ASN][1000 genomes]
rs1994997	0.81[GIH][hapmap]
rs2271483	0.82[EUR][1000 genomes]
rs2643927	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2643930	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2643933	0.91[GIH][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs2729631	1.00[ASW][hapmap];0.89[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2729634	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2729635	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61247260	0.93[ASN][1000 genomes]
rs6487522	0.85[CHB][hapmap]
rs7132820	0.85[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7136804	0.89[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7137379	0.90[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.87[ASN][1000 genomes]
rs7138742	0.82[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.89[TSI][hapmap]
rs7139241	0.90[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs7295585	0.81[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs7299421	0.81[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs7315752	0.91[ASN][1000 genomes]
rs7956992	0.89[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs7963754	0.86[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs7969486	0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs7971906	0.85[ASN][1000 genomes]
rs7977148	0.81[MEX][hapmap]
rs7979763	0.85[CHB][hapmap]

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	nsv898931	chr12:26123345-26192936	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:26169400-26185400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr12:26169600-26182000	Weak transcription	NHLF	lung
3	chr12:26170800-26182000	Weak transcription	Pancreas	Pancrea
4	chr12:26170800-26185600	Weak transcription	Aorta	Aorta
5	chr12:26171000-26182000	Weak transcription	HUVEC	blood vessel
6	chr12:26171000-26183800	Weak transcription	Hela-S3	cervix
7	chr12:26171000-26190600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr12:26172000-26182000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:26172200-26181800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr12:26173400-26186800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr12:26174600-26182000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr12:26174600-26185600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr12:26174800-26181800	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr12:26174800-26182000	Weak transcription	Right Atrium	heart
15	chr12:26174800-26185600	Weak transcription	Ovary	ovary
16	chr12:26175000-26181800	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr12:26175000-26190600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr12:26175000-26191000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr12:26175200-26182000	Weak transcription	Brain Anterior Caudate	brain
20	chr12:26175200-26186800	Weak transcription	Psoas Muscle	Psoas
21	chr12:26175200-26190800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr12:26175400-26181800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr12:26175400-26185800	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr12:26175400-26190000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:26176000-26184200	Weak transcription	Left Ventricle	heart
26	chr12:26179800-26186000	Enhancers	Colon Smooth Muscle	Colon
27	chr12:26180000-26182000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr12:26180000-26182400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr12:26180000-26188200	Enhancers	NHDF-Ad	bronchial
30	chr12:26180200-26188200	Enhancers	Brain Hippocampus Middle	brain
31	chr12:26180400-26182000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr12:26180600-26182000	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr12:26180600-26182000	Weak transcription	Stomach Mucosa	stomach
34	chr12:26180600-26182400	Enhancers	Pancreatic Islets	Pancreatic Islet
35	chr12:26180600-26183800	Enhancers	Brain Cingulate Gyrus	brain
36	chr12:26180600-26184400	Enhancers	Rectal Smooth Muscle	rectum
37	chr12:26180600-26187400	Weak transcription	NH-A	brain
38	chr12:26180800-26181800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr12:26180800-26182200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr12:26180800-26182200	Enhancers	Brain Angular Gyrus	brain
41	chr12:26180800-26188200	Enhancers	Brain Substantia Nigra	brain
42	chr12:26180800-26195000	Weak transcription	HSMM	muscle
43	chr12:26181000-26181800	Active TSS	Fetal Intestine Small	intestine
44	chr12:26181000-26182000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr12:26181000-26182000	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr12:26181000-26182000	Weak transcription	Fetal Lung	lung
47	chr12:26181000-26182000	Weak transcription	Small Intestine	intestine
48	chr12:26181000-26183400	Weak transcription	Fetal Kidney	kidney
49	chr12:26181000-26184200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr12:26181000-26195200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links