Variant report

Variant	rs2282192
Chromosome Location	chr9:100672338-100672339
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:100670192..100672522-chr9:100853837..100856499,2	K562	blood:
2	chr9:100671518..100673484-chr9:100683338..100685757,2	MCF-7	breast:
3	chr9:100647081..100648971-chr9:100671195..100672929,2	K562	blood:
4	chr9:100667967..100674161-chr9:100680279..100686236,11	K562	blood:
5	chr9:100668512..100673720-chr9:100674176..100679549,8	K562	blood:

Variant related genes	Relation type
ENSG00000201830	Chromatin interaction
ENSG00000106785	Chromatin interaction
ENSG00000136932	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10119795	0.88[CHB][hapmap]
rs10760021	0.86[CHB][hapmap];0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs10760022	0.92[ASN][1000 genomes]
rs10984373	0.88[ASN][1000 genomes]
rs10984466	0.90[ASN][1000 genomes]
rs10984506	0.86[ASN][1000 genomes]
rs1127703	0.86[YRI][hapmap]
rs12236440	0.86[YRI][hapmap]
rs12237296	0.85[YRI][hapmap]
rs12238579	0.88[CHB][hapmap]
rs1561958	0.88[CHB][hapmap];0.81[MKK][hapmap]
rs2120263	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2417577	0.94[CHB][hapmap];1.00[CHD][hapmap];0.92[ASN][1000 genomes]
rs3183927	0.94[CHB][hapmap];1.00[CHD][hapmap];0.96[LWK][hapmap];0.82[MKK][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3183928	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3758253	0.94[CHB][hapmap];0.92[ASN][1000 genomes]
rs3758254	0.94[CHB][hapmap];1.00[CHD][hapmap];0.92[ASN][1000 genomes]
rs3780416	0.86[YRI][hapmap]
rs3780420	0.94[CHB][hapmap];1.00[CHD][hapmap];0.96[ASN][1000 genomes]
rs4631576	0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.80[MKK][hapmap];0.92[ASN][1000 genomes]
rs4743147	0.92[CHB][hapmap];0.92[ASN][1000 genomes]
rs55737216	0.92[ASN][1000 genomes]
rs6586	0.88[CHB][hapmap]
rs7864655	0.86[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	nsv893611	chr9:100561055-100739888	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1048135	chr9:100666931-100717030	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
3	nsv525113	chr9:100669799-100686815	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2282192	GALNT12	cis	cerebellum	SCAN
rs2282192	C9orf156	cis	Temporal Cortex	GTEx
rs2282192	FOXE1	cis	Esophagus Mucosa	GTEx
rs2282192	C9orf156	cis	Brain Pons	GTEx
rs2282192	LOC286359	cis	parietal	SCAN
rs2282192	C9orf156	cis	Cerebellum	GTEx
rs2282192	FANCC	cis	parietal	SCAN
rs2282192	C9orf156	cis	parietal	SCAN
rs2282192	C9orf156	cis	cerebellum	SCAN
rs2282192	C9orf156	cis	Frontal Cortex	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100656800-100672400	Weak transcription	Stomach Mucosa	stomach
2	chr9:100658800-100681800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr9:100662800-100684200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr9:100663400-100672600	Weak transcription	A549	lung
5	chr9:100664000-100673200	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr9:100665400-100679000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr9:100665600-100678200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr9:100666600-100675400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr9:100666600-100676000	Strong transcription	Fetal Intestine Large	intestine
10	chr9:100666800-100675800	Strong transcription	Fetal Stomach	stomach
11	chr9:100667000-100675800	Strong transcription	Fetal Intestine Small	intestine
12	chr9:100667200-100679400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:100667200-100684200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr9:100667800-100674000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr9:100668000-100672400	Weak transcription	Fetal Kidney	kidney
16	chr9:100669000-100674600	Weak transcription	HUVEC	blood vessel
17	chr9:100669400-100672800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
18	chr9:100669400-100673000	Strong transcription	Hela-S3	cervix
19	chr9:100669400-100673800	Strong transcription	Aorta	Aorta
20	chr9:100669400-100675800	Strong transcription	Brain Germinal Matrix	brain
21	chr9:100669400-100675800	Strong transcription	Fetal Muscle Leg	muscle
22	chr9:100669600-100673600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr9:100669600-100678600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
24	chr9:100669600-100678800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
25	chr9:100669800-100674800	Genic enhancers	Primary T cells from cord blood	blood
26	chr9:100669800-100675400	Strong transcription	Brain Inferior Temporal Lobe	brain
27	chr9:100669800-100676400	Strong transcription	K562	blood
28	chr9:100669800-100678400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr9:100670000-100673800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr9:100670000-100676200	Strong transcription	Skeletal Muscle Male	skeletal muscle
31	chr9:100670000-100678600	Strong transcription	Duodenum Mucosa	Duodenum
32	chr9:100670000-100684200	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr9:100670200-100673200	Strong transcription	NHLF	lung
34	chr9:100670200-100675400	Strong transcription	Brain Substantia Nigra	brain
35	chr9:100670200-100675800	Strong transcription	Fetal Muscle Trunk	muscle
36	chr9:100670200-100678600	Strong transcription	Liver	Liver
37	chr9:100670200-100678600	Strong transcription	Placenta	Placenta
38	chr9:100670200-100678600	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr9:100670400-100672400	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr9:100670400-100673800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr9:100670400-100675600	Strong transcription	Brain Hippocampus Middle	brain
42	chr9:100670400-100677000	Strong transcription	GM12878-XiMat	blood
43	chr9:100670400-100678400	Strong transcription	Dnd41	blood
44	chr9:100670400-100679400	Strong transcription	Thymus	Thymus
45	chr9:100670600-100674400	Weak transcription	Fetal Brain Male	brain
46	chr9:100670600-100676000	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr9:100670800-100684200	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr9:100671000-100673400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr9:100671000-100673800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr9:100671000-100674200	Genic enhancers	Primary T cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links