Variant report

Variant	rs2297342
Chromosome Location	chr9:78773953-78773954
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:78772507..78774901-chr9:78778089..78780004,2	K562	blood:

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10512055	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11144767	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11144768	0.84[ASN][1000 genomes]
rs11144771	0.83[ASN][1000 genomes]
rs12236697	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12553135	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17776673	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2377526	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2889661	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56295573	0.92[EUR][1000 genomes]
rs56400706	0.92[EUR][1000 genomes]
rs72618110	0.82[ASN][1000 genomes]
rs7357635	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs928355	0.98[ASN][1000 genomes]
rs928356	0.98[ASN][1000 genomes]
rs993001	0.87[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	nsv831627	chr9:78651134-78817669	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
2	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
3	nsv893474	chr9:78753324-78784325	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv893475	chr9:78753324-78817288	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
5	nsv893476	chr9:78768830-78887992	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2297342	TRPM6	cis	parietal	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:78688000-78774000	Weak transcription	Left Ventricle	heart
2	chr9:78757200-78776400	Weak transcription	Psoas Muscle	Psoas
3	chr9:78762800-78780200	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr9:78763400-78776400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:78763800-78776200	Weak transcription	Right Atrium	heart
6	chr9:78765800-78776000	Weak transcription	Fetal Lung	lung
7	chr9:78766400-78776000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr9:78766400-78790000	Weak transcription	Spleen	Spleen
9	chr9:78766600-78774200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr9:78766600-78785200	Weak transcription	Fetal Kidney	kidney
11	chr9:78767400-78776800	Weak transcription	Small Intestine	intestine
12	chr9:78769000-78777000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr9:78770400-78781600	Weak transcription	Brain Substantia Nigra	brain
14	chr9:78770600-78774000	Weak transcription	Lung	lung
15	chr9:78770600-78790000	Weak transcription	Brain Hippocampus Middle	brain
16	chr9:78771000-78790000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr9:78771600-78774400	Strong transcription	Aorta	Aorta
18	chr9:78771600-78790000	Strong transcription	Duodenum Mucosa	Duodenum
19	chr9:78771800-78774000	Weak transcription	NH-A	brain
20	chr9:78771800-78778000	Strong transcription	Primary T cells from cord blood	blood
21	chr9:78771800-78778400	Strong transcription	Sigmoid Colon	Sigmoid Colon
22	chr9:78771800-78779600	Strong transcription	Thymus	Thymus
23	chr9:78771800-78779800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr9:78772000-78774000	Strong transcription	Fetal Muscle Leg	muscle
25	chr9:78772000-78774200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr9:78772000-78775000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr9:78772000-78775200	Strong transcription	Fetal Thymus	thymus
28	chr9:78772000-78775400	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr9:78772200-78776000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr9:78772200-78776000	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr9:78772200-78780000	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr9:78772200-78790000	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr9:78772400-78774000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr9:78772400-78774000	Weak transcription	Brain Cingulate Gyrus	brain
35	chr9:78772400-78777000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr9:78772600-78776000	Weak transcription	Colon Smooth Muscle	Colon
37	chr9:78772600-78777200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr9:78772600-78778600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr9:78772600-78779400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr9:78772600-78790000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr9:78772800-78777000	Weak transcription	Stomach Mucosa	stomach
42	chr9:78773000-78774800	Weak transcription	Fetal Heart	heart
43	chr9:78773000-78790000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr9:78773000-78790000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr9:78773200-78774200	Genic enhancers	Fetal Intestine Large	intestine
46	chr9:78773200-78774200	Strong transcription	Rectal Smooth Muscle	rectum
47	chr9:78773200-78774400	Strong transcription	Stomach Smooth Muscle	stomach
48	chr9:78773200-78775600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr9:78773200-78775600	Strong transcription	Fetal Stomach	stomach
50	chr9:78773200-78776000	Strong transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links