Variant report

Variant	rs706538
Chromosome Location	chr12:26132322-26132323
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:26108836..26112964-chr12:26130309..26134148,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000246695	Chromatin interaction
ENSG00000123094	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10505990	0.82[JPT][hapmap]
rs10842643	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10842644	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10842653	0.88[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11048360	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11048372	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11048378	0.94[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11048379	0.94[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11048380	0.94[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11048381	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11048382	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11048383	0.82[AMR][1000 genomes]
rs11048384	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1120064	1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes]
rs1149804	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11561207	0.81[AMR][1000 genomes]
rs12227689	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12578169	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs12812200	0.81[CHB][hapmap]
rs12812752	0.94[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12813641	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12818478	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12831248	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1390326	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs1513129	0.82[CEU][hapmap]
rs1691889	1.00[CEU][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16929784	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16929817	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16929830	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs16929846	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16929940	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs16929945	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs16929950	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs16929958	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs2055180	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs2132317	0.94[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2279680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2343201	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2643941	0.81[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2669562	0.82[CEU][hapmap]
rs34595529	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35924984	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3803009	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs61622173	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6487525	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs706524	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs706526	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs706531	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs706532	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs706533	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7132590	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7134721	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7298162	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7953171	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7963603	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs829837	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs829987	0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs853656	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758300	chr12:25992331-26161116	Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
2	esv2759886	chr12:25992331-26161116	Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
3	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
4	nsv433521	chr12:26127230-26132785	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv517117	chr12:26127230-26133925	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv522351	chr12:26127230-26149703	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:26117600-26150000	Weak transcription	Hela-S3	cervix
2	chr12:26123800-26134000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:26123800-26134200	Weak transcription	Gastric	stomach
4	chr12:26123800-26137200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:26124400-26138000	Weak transcription	Fetal Intestine Large	intestine
6	chr12:26125000-26138600	Weak transcription	Pancreas	Pancrea
7	chr12:26126800-26134000	Weak transcription	Aorta	Aorta
8	chr12:26128000-26132400	Enhancers	Rectal Smooth Muscle	rectum
9	chr12:26128200-26133000	Enhancers	Left Ventricle	heart
10	chr12:26129400-26134000	Weak transcription	Spleen	Spleen
11	chr12:26129400-26134200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr12:26129400-26139400	Weak transcription	Right Ventricle	heart
13	chr12:26129600-26133000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr12:26129600-26134000	Weak transcription	Esophagus	oesophagus
15	chr12:26129800-26133000	Enhancers	Ovary	ovary
16	chr12:26129800-26134400	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr12:26129800-26143000	Enhancers	Colon Smooth Muscle	Colon
18	chr12:26130000-26132400	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr12:26130000-26133200	Enhancers	Brain Anterior Caudate	brain
20	chr12:26130200-26132400	Enhancers	Fetal Heart	heart
21	chr12:26130200-26132800	Enhancers	Brain Hippocampus Middle	brain
22	chr12:26130200-26132800	Enhancers	Brain Substantia Nigra	brain
23	chr12:26130400-26132400	Enhancers	Brain Angular Gyrus	brain
24	chr12:26130400-26132800	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr12:26130400-26133000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr12:26130800-26132800	Enhancers	Psoas Muscle	Psoas
27	chr12:26130800-26133600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr12:26130800-26134200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr12:26131000-26132600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:26131000-26132600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr12:26131000-26138000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr12:26131000-26139200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:26131000-26145400	Weak transcription	Lung	lung
34	chr12:26131000-26146000	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr12:26131000-26146200	Weak transcription	HSMM	muscle
36	chr12:26131200-26137400	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr12:26131600-26132400	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr12:26131600-26132800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
39	chr12:26131600-26133000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr12:26131600-26133000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr12:26131600-26133000	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr12:26131600-26133000	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr12:26131600-26133200	Weak transcription	Stomach Smooth Muscle	stomach
44	chr12:26131800-26132400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr12:26131800-26132800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr12:26131800-26132800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr12:26131800-26132800	Enhancers	Fetal Lung	lung
48	chr12:26131800-26133000	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr12:26131800-26133000	Enhancers	HUES48 Cell Line	embryonic stem cell
50	chr12:26131800-26133000	Enhancers	HUES6 Cell Line	embryonic stem cell

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