Variant report

Variant	rs2948663
Chromosome Location	chr12:122381194-122381195
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:122367527..122369805-chr12:122380881..122383741,2	K562	blood:
2	chr12:122374906..122377528-chr12:122380651..122382178,2	K562	blood:
3	chr12:122370833..122372465-chr12:122378828..122381354,2	K562	blood:
4	chr12:122380214..122384084-chr12:122388242..122390688,3	K562	blood:
5	chr12:122377347..122378938-chr12:122380678..122382509,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000158023	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1169076	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1169081	0.87[ASN][1000 genomes]
rs1177588	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1179947	0.80[EUR][1000 genomes]
rs1184893	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12578258	0.95[ASN][1000 genomes]
rs12579389	0.95[ASN][1000 genomes]
rs1375653	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1375654	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1375655	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1630699	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1667586	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1678952	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1678953	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1720030	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17852561	0.94[ASN][1000 genomes]
rs2309275	0.88[ASN][1000 genomes]
rs2688411	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2922797	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2948664	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35252940	0.95[ASN][1000 genomes]
rs529736	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs59972569	0.95[ASN][1000 genomes]
rs686220	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7313748	0.95[ASN][1000 genomes]
rs830115	0.87[ASN][1000 genomes]
rs830121	0.81[ASN][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

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122357000-122383600	Weak transcription	Primary T cells from cord blood	blood
2	chr12:122363000-122384800	Weak transcription	Psoas Muscle	Psoas
3	chr12:122363000-122393400	Weak transcription	Brain Angular Gyrus	brain
4	chr12:122363200-122384600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr12:122363600-122383600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr12:122363600-122383800	Weak transcription	Fetal Brain Male	brain
7	chr12:122363600-122385600	Weak transcription	Fetal Lung	lung
8	chr12:122363600-122392200	Weak transcription	Left Ventricle	heart
9	chr12:122363600-122398600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr12:122363600-122408000	Weak transcription	Right Ventricle	heart
11	chr12:122365600-122385800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr12:122365600-122393400	Weak transcription	Brain Substantia Nigra	brain
13	chr12:122365800-122390200	Weak transcription	HUVEC	blood vessel
14	chr12:122365800-122405000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr12:122370600-122387800	Weak transcription	NHDF-Ad	bronchial
16	chr12:122370600-122403200	Weak transcription	Fetal Kidney	kidney
17	chr12:122372200-122396400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr12:122372800-122393600	Weak transcription	Brain Hippocampus Middle	brain
19	chr12:122374000-122402800	Weak transcription	HSMM	muscle
20	chr12:122374000-122405600	Weak transcription	Adipose Nuclei	Adipose
21	chr12:122374800-122382200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr12:122375400-122401400	Weak transcription	Ovary	ovary
23	chr12:122375400-122402600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr12:122375600-122384000	Weak transcription	A549	lung
25	chr12:122375800-122381800	Weak transcription	K562	blood
26	chr12:122375800-122384000	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr12:122375800-122385800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr12:122375800-122393600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr12:122375800-122415800	Weak transcription	Liver	Liver
30	chr12:122376000-122382000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr12:122376000-122388000	Weak transcription	NHLF	lung
32	chr12:122376000-122393400	Weak transcription	Brain Anterior Caudate	brain
33	chr12:122376000-122401600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr12:122376000-122413000	Weak transcription	Aorta	Aorta
35	chr12:122377400-122381800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr12:122377400-122383200	Weak transcription	Fetal Intestine Small	intestine
37	chr12:122377400-122406200	Weak transcription	Thymus	Thymus
38	chr12:122378200-122382200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr12:122378600-122384400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr12:122378800-122384200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr12:122379400-122383200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr12:122379800-122382200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr12:122379800-122382200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr12:122379800-122382400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr12:122380200-122383000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr12:122380600-122381200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr12:122380600-122384400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr12:122380600-122387800	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr12:122380600-122401600	Weak transcription	Pancreas	Pancrea
50	chr12:122380800-122382200	Genic enhancers	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links