Variant report

Variant	rs11043271
Chromosome Location	chr12:122394921-122394922
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:122392364..122395204-chr12:122467320..122469224,2	K562	blood:
2	chr12:122390662..122395297-chr12:122466472..122469968,4	MCF-7	breast:
3	chr12:122393562..122396353-chr12:122460972..122463920,2	K562	blood:
4	chr12:122393592..122395779-chr12:122400656..122403431,2	MCF-7	breast:
5	chr12:122391300..122395865-chr12:122397802..122402180,6	K562	blood:
6	chr12:122393570..122396263-chr12:122456754..122459004,2	MCF-7	breast:
7	chr12:122392019..122395422-chr12:122459047..122461618,4	MCF-7	breast:
8	chr12:122394365..122397309-chr12:122398081..122400536,2	K562	blood:
9	chr12:122393647..122395648-chr12:122451452..122452969,2	MCF-7	breast:
10	chr12:122394265..122395832-chr12:122468104..122470419,2	MCF-7	breast:
11	chr12:122394100..122396317-chr12:122458404..122460674,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000255856	Chromatin interaction
ENSG00000110987	Chromatin interaction
ENSG00000158023	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10840630	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840631	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840632	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840633	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840637	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11043220	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs11043223	1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap]
rs11043225	1.00[ASN][1000 genomes]
rs11043233	0.96[CEU][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11043242	0.96[CEU][hapmap]
rs11043243	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11043244	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11043246	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11043251	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11043275	0.83[EUR][1000 genomes]
rs11043278	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11043280	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11043288	1.00[ASW][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1154514	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11612028	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1169070	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1169071	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11833399	1.00[CHD][hapmap]
rs12369331	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12809676	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12817066	0.81[EUR][1000 genomes]
rs12822775	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12823194	1.00[ASN][1000 genomes]
rs12824593	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12825161	1.00[ASN][1000 genomes]
rs12827036	1.00[ASW][hapmap];1.00[CHD][hapmap];0.90[LWK][hapmap];0.89[MEX][hapmap]
rs12829688	0.83[EUR][1000 genomes]
rs1720033	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1720037	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2167067	1.00[ASN][1000 genomes]
rs34159444	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34906460	1.00[ASN][1000 genomes]
rs35244551	0.84[AMR][1000 genomes]
rs3847694	0.96[CEU][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap]
rs66611928	0.84[AFR][1000 genomes]
rs66751701	1.00[ASN][1000 genomes]
rs7132055	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7137218	0.96[CEU][hapmap];0.91[TSI][hapmap]
rs7313252	0.96[CEU][hapmap]
rs73217776	1.00[ASN][1000 genomes]
rs7954584	0.90[MEX][hapmap]
rs9739381	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv899568	chr12:122254713-122456524	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	esv34001	chr12:122298737-122521637	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	esv1799099	chr12:122382229-122398494	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11043271	CCDC60	cis	cerebellum	SCAN
rs11043271	OGFOD2	cis	cerebellum	SCAN
rs11043271	WDR66	cis	cerebellum	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122363600-122398600	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr12:122363600-122408000	Weak transcription	Right Ventricle	heart
3	chr12:122365800-122405000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr12:122370600-122403200	Weak transcription	Fetal Kidney	kidney
5	chr12:122372200-122396400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:122374000-122402800	Weak transcription	HSMM	muscle
7	chr12:122374000-122405600	Weak transcription	Adipose Nuclei	Adipose
8	chr12:122375400-122401400	Weak transcription	Ovary	ovary
9	chr12:122375400-122402600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr12:122375800-122415800	Weak transcription	Liver	Liver
11	chr12:122376000-122401600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr12:122376000-122413000	Weak transcription	Aorta	Aorta
13	chr12:122377400-122406200	Weak transcription	Thymus	Thymus
14	chr12:122380600-122401600	Weak transcription	Pancreas	Pancrea
15	chr12:122380800-122405800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr12:122381000-122396400	Weak transcription	Stomach Smooth Muscle	stomach
17	chr12:122381000-122400000	Weak transcription	Spleen	Spleen
18	chr12:122381000-122405800	Weak transcription	Fetal Muscle Leg	muscle
19	chr12:122382200-122396200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr12:122382200-122402200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr12:122382600-122399600	Weak transcription	K562	blood
22	chr12:122384800-122396400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr12:122386200-122398600	Weak transcription	Fetal Stomach	stomach
24	chr12:122388200-122395800	Weak transcription	HSMMtube	muscle
25	chr12:122388200-122396800	Weak transcription	NHDF-Ad	bronchial
26	chr12:122388200-122398600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr12:122388400-122395000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr12:122388400-122396400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr12:122388400-122399800	Weak transcription	NHLF	lung
30	chr12:122388400-122401800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr12:122389200-122396200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr12:122389200-122396400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr12:122389600-122395800	Weak transcription	HMEC	breast
34	chr12:122391400-122410800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr12:122391600-122402800	Weak transcription	A549	lung
36	chr12:122391600-122405600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr12:122391800-122395600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr12:122391800-122410800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr12:122392000-122397200	Weak transcription	HepG2	liver
40	chr12:122392200-122396400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr12:122393200-122398600	Strong transcription	NHEK	skin
42	chr12:122393200-122402000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr12:122393400-122399000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr12:122393800-122395200	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr12:122393800-122396000	Weak transcription	Brain Anterior Caudate	brain
46	chr12:122394000-122395600	Weak transcription	Brain Germinal Matrix	brain
47	chr12:122394000-122396600	Weak transcription	Osteobl	bone
48	chr12:122394000-122429800	Weak transcription	Brain Cingulate Gyrus	brain
49	chr12:122394200-122395800	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr12:122394200-122396200	Weak transcription	Brain Hippocampus Middle	brain

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