Variant report

Variant	rs17732089
Chromosome Location	chr12:63023658-63023659
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:62996090..62998530-chr12:63021670..63024116,3	MCF-7	breast:
2	chr12:63017661..63021132-chr12:63021138..63024799,3	K562	blood:
3	chr12:63023335..63025225-chr12:63026338..63028730,2	K562	blood:

Variant related genes	Relation type
ENSG00000199179	Chromatin interaction
ENSG00000257354	Chromatin interaction
ENSG00000221949	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10444576	1.00[JPT][hapmap]
rs10877855	0.82[AFR][1000 genomes]
rs10877856	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes]
rs10877857	0.80[CEU][hapmap];0.82[AFR][1000 genomes]
rs10877859	0.80[CEU][hapmap];0.82[AFR][1000 genomes]
rs10877862	0.82[AFR][1000 genomes]
rs10877864	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.82[AFR][1000 genomes]
rs10877870	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs11174487	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs11174494	0.82[AFR][1000 genomes]
rs11174495	0.82[AFR][1000 genomes]
rs11174498	0.82[AFR][1000 genomes]
rs11174504	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes]
rs11174514	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes]
rs11174517	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.82[AFR][1000 genomes]
rs11174518	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes]
rs11174527	0.81[EUR][1000 genomes]
rs11174537	0.82[EUR][1000 genomes]
rs11174557	0.94[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11174562	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11174568	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174569	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174575	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174576	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174583	1.00[MEX][hapmap];0.97[MKK][hapmap]
rs11174588	1.00[MEX][hapmap]
rs11520127	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11613132	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs11614022	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes]
rs11614822	0.82[EUR][1000 genomes]
rs12367878	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12369751	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12369961	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12369985	1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs12370404	0.80[EUR][1000 genomes]
rs12580567	1.00[CHB][hapmap]
rs17731893	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MKK][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17732182	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2270732	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs55833440	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7296573	0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7297093	0.93[CEU][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7301016	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes]
rs7302094	1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7302456	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7302602	1.00[MEX][hapmap];0.97[MKK][hapmap]
rs7303825	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs7311952	1.00[JPT][hapmap]
rs73124315	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73126004	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs73126024	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73141045	0.82[EUR][1000 genomes]
rs7962519	0.91[CEU][hapmap];0.82[AFR][1000 genomes]
rs7975109	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17732089	OS9	cis	parietal	SCAN
rs17732089	MON2	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:62999400-63025000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:63000800-63024200	Weak transcription	Fetal Brain Female	brain
3	chr12:63003200-63023800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr12:63007800-63024800	Weak transcription	NH-A	brain
5	chr12:63010200-63025200	Weak transcription	HSMMtube	muscle
6	chr12:63012400-63023800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr12:63013800-63025200	Weak transcription	Right Atrium	heart
8	chr12:63019400-63025000	Weak transcription	Adipose Nuclei	Adipose
9	chr12:63019600-63025400	Weak transcription	Pancreas	Pancrea
10	chr12:63019800-63025200	Weak transcription	Liver	Liver
11	chr12:63019800-63025800	Weak transcription	Placenta	Placenta
12	chr12:63021200-63024000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr12:63021400-63025200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:63021800-63024000	Weak transcription	HMEC	breast
15	chr12:63022200-63025600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr12:63022400-63023800	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr12:63022400-63023800	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr12:63022400-63024200	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr12:63022400-63024200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr12:63022400-63024600	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr12:63022600-63023800	Enhancers	H1 Cell Line	embryonic stem cell
22	chr12:63022600-63023800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr12:63022600-63024600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr12:63022600-63025400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:63022600-63027000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr12:63022800-63024200	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr12:63022800-63024400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr12:63022800-63024600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr12:63023000-63025000	Enhancers	Osteobl	bone
30	chr12:63023200-63024000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr12:63023200-63024000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr12:63023200-63024400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr12:63023200-63024800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:63023400-63023800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr12:63023400-63025000	Enhancers	A549	lung
36	chr12:63023600-63023800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
37	chr12:63023600-63023800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr12:63023600-63024400	Weak transcription	Fetal Brain Male	brain
39	chr12:63023600-63025000	Enhancers	NHDF-Ad	bronchial
40	chr12:63023600-63025400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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