Variant report

Variant	rs12378822
Chromosome Location	chr9:79069563-79069564
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10869781	0.90[ASN][1000 genomes]
rs11144905	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11144908	0.90[ASN][1000 genomes]
rs11144909	0.90[ASN][1000 genomes]
rs12351617	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12380332	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1324212	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs57339182	0.85[ASN][1000 genomes]
rs57429014	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58651349	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59322809	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62564441	0.86[EUR][1000 genomes]
rs62564442	0.88[EUR][1000 genomes]
rs62564444	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62564446	0.85[ASN][1000 genomes]
rs62564449	0.90[ASN][1000 genomes]
rs62564454	0.90[ASN][1000 genomes]
rs62565109	0.85[ASN][1000 genomes]
rs6560524	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7854540	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[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	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893478	chr9:78933874-79101006	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv893479	chr9:78971253-79275226	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79063000-79070800	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr9:79064600-79071000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr9:79066200-79071000	Weak transcription	A549	lung
4	chr9:79066600-79070800	Weak transcription	HSMMtube	muscle
5	chr9:79066600-79073600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr9:79066800-79070800	Weak transcription	NH-A	brain
7	chr9:79066800-79071000	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr9:79066800-79071200	Weak transcription	HMEC	breast
9	chr9:79067800-79069800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr9:79067800-79071200	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr9:79068000-79069600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr9:79068000-79069600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr9:79068000-79071600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr9:79068200-79071000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr9:79068200-79071200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr9:79068200-79071400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr9:79068400-79069600	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr9:79068400-79071000	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr9:79068400-79071000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr9:79068400-79071200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr9:79068600-79071200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr9:79068600-79073600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr9:79068800-79069600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr9:79068800-79070000	Weak transcription	Primary hematopoietic stem cells	blood
25	chr9:79068800-79071000	Weak transcription	HSMM	muscle
26	chr9:79068800-79071000	Weak transcription	NHLF	lung
27	chr9:79068800-79071400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr9:79069000-79071000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr9:79069000-79071000	Weak transcription	Placenta	Placenta
30	chr9:79069200-79070800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr9:79069200-79070800	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr9:79069200-79070800	Weak transcription	Osteobl	bone
33	chr9:79069400-79069600	Enhancers	Gastric	stomach
34	chr9:79069400-79069800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr9:79069400-79071200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr9:79069400-79071200	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr9:79069400-79073400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links