Variant report

Variant	rs1169072
Chromosome Location	chr12:122401501-122401502
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:122383104..122386002-chr12:122399746..122401502,2	K562	blood:
2	chr12:122400159..122402861-chr12:122407797..122409946,2	MCF-7	breast:
3	chr12:122393592..122395779-chr12:122400656..122403431,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000158023	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10743186	0.81[EUR][1000 genomes]
rs10770186	0.96[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs11043242	0.81[CEU][hapmap]
rs11043250	0.93[ASN][1000 genomes]
rs6486782	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1169072	WDR66	cis	cerebellum	SCAN
rs1169072	CCDC60	cis	cerebellum	SCAN
rs1169072	FBXO21	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122363600-122408000	Weak transcription	Right Ventricle	heart
2	chr12:122365800-122405000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr12:122370600-122403200	Weak transcription	Fetal Kidney	kidney
4	chr12:122374000-122402800	Weak transcription	HSMM	muscle
5	chr12:122374000-122405600	Weak transcription	Adipose Nuclei	Adipose
6	chr12:122375400-122402600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr12:122375800-122415800	Weak transcription	Liver	Liver
8	chr12:122376000-122401600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr12:122376000-122413000	Weak transcription	Aorta	Aorta
10	chr12:122377400-122406200	Weak transcription	Thymus	Thymus
11	chr12:122380600-122401600	Weak transcription	Pancreas	Pancrea
12	chr12:122380800-122405800	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr12:122381000-122405800	Weak transcription	Fetal Muscle Leg	muscle
14	chr12:122382200-122402200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr12:122388400-122401800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr12:122391400-122410800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr12:122391600-122402800	Weak transcription	A549	lung
18	chr12:122391600-122405600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr12:122391800-122410800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr12:122393200-122402000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr12:122394000-122429800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr12:122394200-122402800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr12:122394200-122407600	Weak transcription	Brain Angular Gyrus	brain
24	chr12:122394200-122411000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr12:122394200-122411200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr12:122396000-122408000	Weak transcription	Fetal Intestine Small	intestine
27	chr12:122396400-122401800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr12:122396600-122408200	Weak transcription	Fetal Brain Female	brain
29	chr12:122396600-122439200	Weak transcription	Brain Anterior Caudate	brain
30	chr12:122396800-122402800	Weak transcription	NH-A	brain
31	chr12:122396800-122410800	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr12:122397200-122402600	Weak transcription	NHDF-Ad	bronchial
33	chr12:122397200-122403000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr12:122397200-122406000	Weak transcription	Brain Hippocampus Middle	brain
35	chr12:122397200-122408400	Weak transcription	Brain Substantia Nigra	brain
36	chr12:122397600-122403000	Weak transcription	Stomach Smooth Muscle	stomach
37	chr12:122397600-122406000	Weak transcription	Esophagus	oesophagus
38	chr12:122398600-122402000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr12:122398800-122402000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr12:122398800-122406200	Weak transcription	Fetal Thymus	thymus
41	chr12:122399000-122402000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr12:122399000-122411000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr12:122399000-122411000	Weak transcription	Gastric	stomach
44	chr12:122399800-122402000	Strong transcription	NHLF	lung
45	chr12:122400000-122402000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr12:122400000-122402000	Strong transcription	Spleen	Spleen
47	chr12:122400200-122401800	Strong transcription	NHEK	skin
48	chr12:122400200-122404800	Weak transcription	K562	blood
49	chr12:122400200-122408200	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr12:122400400-122401600	Weak transcription	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links