Variant report

Variant	rs1500875
Chromosome Location	chr12:32659527-32659528
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:32550963..32552708-chr12:32659377..32661100,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139132	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10506090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10506093	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10771960	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10771961	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10771962	0.84[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10844222	0.86[CEU][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10844223	0.82[CEU][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10844224	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10844226	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10844227	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10844228	0.95[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10844229	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10844230	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10844231	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10844232	0.89[ASN][1000 genomes]
rs10844234	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11052040	0.89[ASN][1000 genomes]
rs11052041	0.91[ASN][1000 genomes]
rs11052042	0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11052046	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11052052	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11052053	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11052055	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs11052079	1.00[JPT][hapmap]
rs11608343	0.95[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12366886	0.89[ASN][1000 genomes]
rs1500876	0.86[CEU][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16920058	1.00[JPT][hapmap]
rs16920125	1.00[JPT][hapmap]
rs17536908	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1909509	1.00[JPT][hapmap]
rs2036266	0.81[ASN][1000 genomes]
rs2133943	0.82[CEU][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2133944	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4105685	0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4520681	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61928965	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7308163	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73092002	0.93[ASN][1000 genomes]
rs73094103	0.93[ASN][1000 genomes]
rs7953022	0.89[ASN][1000 genomes]
rs7962342	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7964715	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7967306	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7967702	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7970857	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7974089	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7977101	0.89[ASN][1000 genomes]
rs7980571	0.89[ASN][1000 genomes]
rs9943832	0.88[YRI][hapmap]

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	nsv531960	chr12:32257285-32775277	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	esv2751096	chr12:32280340-32702784	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1054191	chr12:32534619-32733066	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv541455	chr12:32534619-32733066	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	esv3342938	chr12:32551041-32716745	Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv898970	chr12:32622097-32680236	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1500875	SEC14L2	trans	parietal	SCAN
rs1500875	FGD4	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32649000-32660800	Weak transcription	Thymus	Thymus
2	chr12:32655200-32661600	Weak transcription	Spleen	Spleen
3	chr12:32655200-32686000	Weak transcription	Lung	lung
4	chr12:32655400-32661000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr12:32656000-32661000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr12:32656000-32666000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr12:32656000-32668000	Weak transcription	Fetal Thymus	thymus
8	chr12:32656200-32659800	Enhancers	H1 Cell Line	embryonic stem cell
9	chr12:32656200-32662600	Weak transcription	HepG2	liver
10	chr12:32656200-32668000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr12:32656400-32659800	Enhancers	Fetal Lung	lung
12	chr12:32656400-32660000	Enhancers	Fetal Intestine Small	intestine
13	chr12:32656400-32685800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr12:32656800-32659800	Enhancers	Fetal Intestine Large	intestine
15	chr12:32657000-32659600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr12:32657000-32659600	Enhancers	Psoas Muscle	Psoas
17	chr12:32657000-32661000	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr12:32657000-32661800	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr12:32657200-32659800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr12:32657200-32662200	Enhancers	Fetal Heart	heart
21	chr12:32657400-32659600	Enhancers	Liver	Liver
22	chr12:32657400-32659800	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr12:32657400-32661400	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr12:32657600-32659600	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr12:32657800-32659600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr12:32658000-32659600	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr12:32658000-32659600	Enhancers	Ovary	ovary
28	chr12:32658200-32659600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr12:32658200-32659600	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr12:32658200-32659800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:32658400-32659600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr12:32658400-32659600	Enhancers	Brain Germinal Matrix	brain
33	chr12:32658400-32660400	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr12:32658400-32660800	Weak transcription	Brain Angular Gyrus	brain
35	chr12:32658400-32660800	Weak transcription	Right Ventricle	heart
36	chr12:32658400-32661000	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr12:32658600-32659800	Enhancers	Brain Anterior Caudate	brain
38	chr12:32658600-32659800	Enhancers	Brain Hippocampus Middle	brain
39	chr12:32658600-32660800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr12:32658600-32667800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr12:32658600-32682000	Weak transcription	Fetal Muscle Trunk	muscle
42	chr12:32658800-32659600	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr12:32658800-32659600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr12:32658800-32659600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr12:32658800-32659600	Enhancers	Fetal Muscle Leg	muscle
46	chr12:32658800-32659600	Enhancers	Fetal Stomach	stomach
47	chr12:32658800-32659600	Enhancers	Left Ventricle	heart
48	chr12:32658800-32659600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
49	chr12:32658800-32660800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr12:32659000-32659600	Enhancers	Esophagus	oesophagus

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