Variant report

Variant	rs7980188
Chromosome Location	chr12:118521290-118521291
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:118521252-118521355	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
VSIG10	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10850956	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4767659	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4767660	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4767661	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4767662	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4767663	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6490164	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7301598	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7301776	0.91[EUR][1000 genomes]
rs7488514	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7969236	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][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	nsv1053785	chr12:118490955-118874194	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv560389	chr12:118502467-118564087	Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv899546	chr12:118515230-118563982	Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118500600-118535200	Weak transcription	Brain Substantia Nigra	brain
2	chr12:118500800-118526400	Weak transcription	HMEC	breast
3	chr12:118500800-118539600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr12:118500800-118539800	Weak transcription	Right Ventricle	heart
5	chr12:118500800-118540800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr12:118501000-118525600	Weak transcription	Fetal Brain Female	brain
7	chr12:118501000-118527400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr12:118501000-118530600	Weak transcription	Brain Angular Gyrus	brain
9	chr12:118501000-118533800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr12:118501000-118539600	Weak transcription	Psoas Muscle	Psoas
11	chr12:118501000-118540200	Weak transcription	HUVEC	blood vessel
12	chr12:118501000-118540800	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr12:118501000-118540800	Weak transcription	NH-A	brain
14	chr12:118501200-118526400	Weak transcription	Small Intestine	intestine
15	chr12:118501200-118536000	Weak transcription	Right Atrium	heart
16	chr12:118501200-118540400	Weak transcription	Brain Germinal Matrix	brain
17	chr12:118501200-118540800	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr12:118501200-118541000	Weak transcription	Aorta	Aorta
19	chr12:118501600-118540400	Weak transcription	NHLF	lung
20	chr12:118501800-118527000	Weak transcription	NHEK	skin
21	chr12:118501800-118533200	Weak transcription	Hela-S3	cervix
22	chr12:118502200-118540800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr12:118502200-118540800	Weak transcription	Brain Anterior Caudate	brain
24	chr12:118502600-118536200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr12:118503200-118521800	Weak transcription	Stomach Mucosa	stomach
26	chr12:118509000-118538400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr12:118509200-118528000	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr12:118509400-118528800	Weak transcription	NHDF-Ad	bronchial
29	chr12:118511800-118534400	Weak transcription	Fetal Muscle Trunk	muscle
30	chr12:118511800-118539600	Weak transcription	Pancreas	Pancrea
31	chr12:118513400-118522000	Strong transcription	H1 Cell Line	embryonic stem cell
32	chr12:118513400-118523400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr12:118513400-118534200	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr12:118514600-118540400	Weak transcription	Fetal Heart	heart
35	chr12:118515800-118521600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr12:118515800-118526200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr12:118515800-118540800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr12:118515800-118540800	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr12:118516000-118539800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr12:118517400-118526200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr12:118517400-118526200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr12:118517400-118535600	Weak transcription	Colonic Mucosa	Colon
43	chr12:118517600-118521800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr12:118517600-118526200	Weak transcription	A549	lung
45	chr12:118517600-118535800	Weak transcription	Placenta	Placenta
46	chr12:118517600-118540000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr12:118517600-118540800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr12:118517600-118540800	Weak transcription	Stomach Smooth Muscle	stomach
49	chr12:118517800-118528400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr12:118518600-118540000	Weak transcription	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links