Variant report

Variant	rs704217
Chromosome Location	chr12:22047174-22047175
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	chr12:22041351..22043151-chr12:22046321..22048748,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10743426	0.83[GIH][hapmap]
rs10770871	0.81[GIH][hapmap]
rs12304313	0.83[JPT][hapmap];0.81[AMR][1000 genomes]
rs1421602	0.81[GIH][hapmap]
rs2131136	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2277405	0.81[GIH][hapmap]
rs2292772	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4148654	0.81[GIH][hapmap]
rs4148655	0.81[CEU][hapmap]
rs4148660	0.81[GIH][hapmap]
rs4148664	0.83[JPT][hapmap];0.87[MEX][hapmap];0.82[AMR][1000 genomes]
rs59061211	0.85[ASN][1000 genomes]
rs704215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7137730	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7138546	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7301876	0.83[JPT][hapmap];0.82[AMR][1000 genomes]
rs7308718	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[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	nsv557741	chr12:21578559-22169854	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1051073	chr12:21910875-22271209	Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv470275	chr12:21938544-22126314	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv898900	chr12:22044843-22083212	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv898901	chr12:22047174-22075960	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv898902	chr12:22047174-22083212	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs704217	ABCC9	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:22035200-22058600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr12:22035200-22092200	Weak transcription	Fetal Muscle Leg	muscle
3	chr12:22041600-22050600	Weak transcription	Fetal Lung	lung
4	chr12:22044000-22047200	Enhancers	Rectal Smooth Muscle	rectum
5	chr12:22044400-22048400	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr12:22044800-22049400	Enhancers	Colon Smooth Muscle	Colon
7	chr12:22045000-22059200	Weak transcription	Left Ventricle	heart
8	chr12:22045200-22047800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr12:22045200-22053800	Weak transcription	Right Ventricle	heart
10	chr12:22045200-22058800	Weak transcription	Fetal Muscle Trunk	muscle
11	chr12:22045400-22064800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr12:22045600-22047800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr12:22045600-22047800	Enhancers	Stomach Smooth Muscle	stomach
14	chr12:22045600-22049200	Weak transcription	Fetal Stomach	stomach
15	chr12:22045600-22053000	Weak transcription	Aorta	Aorta
16	chr12:22045600-22059200	Weak transcription	NHLF	lung
17	chr12:22045600-22064800	Weak transcription	Fetal Heart	heart
18	chr12:22046000-22059000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr12:22046200-22047200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:22046600-22047600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr12:22046600-22047600	Weak transcription	Adipose Nuclei	Adipose
22	chr12:22046800-22047200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
23	chr12:22047000-22047800	Flanking Active TSS	Liver	Liver
24	chr12:22047000-22048000	Enhancers	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links