Variant report

Variant	rs11168369
Chromosome Location	chr12:48431168-48431169
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48426470..48428398-chr12:48428806..48432334,3	MCF-7	breast:
2	chr12:48377455..48379308-chr12:48429831..48432694,2	K562	blood:
3	chr12:48426621..48428717-chr12:48430919..48432434,2	K562	blood:
4	chr12:48425840..48427385-chr12:48429084..48431301,2	MCF-7	breast:
5	chr12:48422786..48426072-chr12:48430482..48433177,3	MCF-7	breast:
6	chr12:48428906..48431676-chr12:48435313..48438563,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139219	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10082861	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs10219623	1.00[JPT][hapmap]
rs10467101	0.84[JPT][hapmap]
rs10875720	0.91[ASN][1000 genomes]
rs10875722	0.91[ASN][1000 genomes]
rs10875723	0.92[ASN][1000 genomes]
rs10875724	0.85[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10875725	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10875728	0.97[EUR][1000 genomes]
rs10875729	0.97[EUR][1000 genomes]
rs10875730	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875731	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875732	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875735	0.92[CEU][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10875736	0.81[AFR][1000 genomes]
rs10875737	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10875738	0.82[EUR][1000 genomes]
rs10875740	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10875745	1.00[JPT][hapmap]
rs10875746	1.00[JPT][hapmap]
rs10875747	0.82[EUR][1000 genomes]
rs10875748	0.82[EUR][1000 genomes]
rs10875750	0.86[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10875767	0.93[JPT][hapmap]
rs10875770	0.93[JPT][hapmap]
rs10875772	0.93[JPT][hapmap]
rs11168355	0.94[CHB][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11168357	0.94[CHB][hapmap];0.93[JPT][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11168370	0.98[EUR][1000 genomes]
rs11168371	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168383	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11168386	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11168401	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11168403	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs11168413	1.00[JPT][hapmap]
rs11168414	0.86[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs11168418	0.86[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs11168420	0.86[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs11168421	1.00[JPT][hapmap]
rs11168425	1.00[JPT][hapmap]
rs11168427	0.86[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11168433	0.86[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11168450	1.00[JPT][hapmap]
rs11168459	0.93[JPT][hapmap]
rs12228854	0.82[YRI][hapmap]
rs12296244	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12297004	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12297470	1.00[JPT][hapmap]
rs12301339	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12304476	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12305182	0.83[CHB][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12305511	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs12306451	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12310813	1.00[JPT][hapmap]
rs12310999	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12311774	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12311953	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12312134	0.93[JPT][hapmap]
rs12313300	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12313404	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12315625	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs17122620	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17122666	0.86[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs17122812	0.93[JPT][hapmap]
rs1859445	1.00[JPT][hapmap]
rs2012773	1.00[JPT][hapmap]
rs2079295	0.92[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs2107638	1.00[JPT][hapmap]
rs2158516	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2228500	0.86[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs2269933	1.00[JPT][hapmap]
rs2269935	0.86[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs2269936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286021	0.82[EUR][1000 genomes]
rs28459711	0.91[ASN][1000 genomes]
rs3782910	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3782911	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3809322	0.83[YRI][hapmap]
rs4760609	0.85[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4760610	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4760619	1.00[JPT][hapmap]
rs4760622	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs4760676	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4760680	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4760681	0.86[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs4760687	1.00[JPT][hapmap]
rs4760695	0.81[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4760696	1.00[JPT][hapmap]
rs4760697	1.00[JPT][hapmap]
rs58952582	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60761335	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61918774	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61918806	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs61918809	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs61918810	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6580659	1.00[JPT][hapmap]
rs7135779	1.00[JPT][hapmap]
rs719008	0.94[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs725454	0.86[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs7299135	0.94[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs7299271	0.94[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs7299364	0.91[ASN][1000 genomes]
rs73102065	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs73102067	0.81[AFR][1000 genomes]
rs7486424	1.00[JPT][hapmap]
rs7964359	0.81[CHB][hapmap];0.82[ASN][1000 genomes]
rs8804	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs886588	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs989144	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11168369	RP1-228P16.1	cis	Heart Left Ventricle	GTEx
rs11168369	RP1-228P16.1	cis	Artery Tibial	GTEx
rs11168369	RP1-228P16.1	cis	Skin Sun Exposed Lower leg	GTEx
rs11168369	RP1-228P16.1	cis	Adipose Subcutaneous	GTEx
rs11168369	RP1-228P16.1	cis	Thyroid	GTEx

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48422800-48438800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr12:48424800-48437400	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr12:48427600-48435600	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr12:48428600-48432200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:48429000-48434200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr12:48429200-48433600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr12:48429200-48437000	Weak transcription	GM12878-XiMat	blood
8	chr12:48429400-48433200	Weak transcription	Colonic Mucosa	Colon
9	chr12:48429400-48435400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:48429600-48436400	Weak transcription	HMEC	breast
11	chr12:48429800-48434200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr12:48430000-48431200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr12:48430200-48432000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:48430200-48433200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr12:48430400-48431600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
16	chr12:48430400-48432200	Enhancers	H9 Cell Line	embryonic stem cell
17	chr12:48430600-48431200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:48430600-48431200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr12:48430600-48431200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
20	chr12:48430600-48431200	Enhancers	HSMMtube	muscle
21	chr12:48430600-48431800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr12:48430600-48431800	Enhancers	Fetal Muscle Trunk	muscle
23	chr12:48430600-48431800	Enhancers	Placenta	Placenta
24	chr12:48430600-48431800	Enhancers	Lung	lung
25	chr12:48430600-48431800	Enhancers	Right Atrium	heart
26	chr12:48430600-48431800	Enhancers	K562	blood
27	chr12:48430600-48432000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr12:48430600-48432000	Enhancers	Fetal Intestine Small	intestine
29	chr12:48430600-48432000	Enhancers	Fetal Kidney	kidney
30	chr12:48430600-48432000	Enhancers	Fetal Lung	lung
31	chr12:48430600-48432000	Enhancers	Ovary	ovary
32	chr12:48430600-48432000	Enhancers	Right Ventricle	heart
33	chr12:48430600-48432200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr12:48430600-48432200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr12:48430600-48432200	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr12:48430600-48432200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr12:48430600-48432400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr12:48430800-48431200	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
39	chr12:48430800-48431200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr12:48430800-48431400	Enhancers	NH-A	brain
41	chr12:48430800-48431600	Weak transcription	Pancreas	Pancrea
42	chr12:48430800-48431800	Enhancers	Fetal Muscle Leg	muscle
43	chr12:48430800-48431800	Enhancers	Fetal Stomach	stomach
44	chr12:48430800-48432000	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr12:48430800-48432000	Enhancers	Fetal Thymus	thymus
46	chr12:48430800-48432800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr12:48431000-48431200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
48	chr12:48431000-48431200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr12:48431000-48431400	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
50	chr12:48431000-48431400	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell

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