Variant report

Variant	rs2274653
Chromosome Location	chr9:98691257-98691258
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	chr9:98636561..98638222-chr9:98688892..98691285,2	K562	blood:

Variant related genes	Relation type
ENSG00000175611	Chromatin interaction
ENSG00000182150	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10988581	0.82[EUR][1000 genomes]
rs10988792	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10988804	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11787559	0.96[AFR][1000 genomes]
rs11790491	0.81[EUR][1000 genomes]
rs11794054	0.82[EUR][1000 genomes]
rs12001	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12683310	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12685318	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12685807	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16910298	0.81[EUR][1000 genomes]
rs2026032	0.91[YRI][hapmap];0.99[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2069053	0.81[EUR][1000 genomes]
rs2274654	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3802438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4743391	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743400	0.84[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4743418	0.82[EUR][1000 genomes]
rs4743419	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs591486	0.81[YRI][hapmap]
rs73536517	0.82[EUR][1000 genomes]
rs7868270	0.81[EUR][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	nsv482884	chr9:98530027-98691937	Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv893599	chr9:98542410-98991254	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
3	nsv893600	chr9:98608989-98775459	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	esv1801890	chr9:98660433-98701801	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2274653	C9orf130	Cis_1M	lymphoblastoid	RTeQTL
rs2274653	C9orf130	cis	lesional skin	skin_eQTL
rs2274653	LINC00476	cis	Esophagus Mucosa	GTEx
rs2274653	LINC00476	cis	Whole Blood	GTEx
rs2274653	LINC00476	cis	Esophagus Muscularis	GTEx
rs2274653	LINC00476	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98638800-98702200	Weak transcription	Pancreas	Pancrea
2	chr9:98640000-98718600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr9:98645800-98702200	Weak transcription	Aorta	Aorta
4	chr9:98649400-98694400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr9:98649400-98718600	Weak transcription	Spleen	Spleen
6	chr9:98660000-98706000	Weak transcription	Fetal Heart	heart
7	chr9:98673600-98702200	Weak transcription	Small Intestine	intestine
8	chr9:98675400-98718600	Weak transcription	Esophagus	oesophagus
9	chr9:98676600-98693200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr9:98677600-98709000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr9:98678000-98699200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr9:98678000-98699600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr9:98678600-98705600	Weak transcription	Psoas Muscle	Psoas
14	chr9:98678800-98718600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr9:98679400-98695200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr9:98679400-98698600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr9:98680800-98706000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr9:98681800-98694400	Weak transcription	Fetal Stomach	stomach
19	chr9:98681800-98736600	Weak transcription	Colonic Mucosa	Colon
20	chr9:98682400-98698000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr9:98683200-98697800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr9:98683400-98702600	Strong transcription	HSMM	muscle
23	chr9:98684000-98691800	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr9:98684200-98697200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr9:98684800-98695400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr9:98684800-98697800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr9:98685400-98699600	Strong transcription	Primary T cells from cord blood	blood
28	chr9:98685800-98698400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr9:98686000-98699200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr9:98686200-98699400	Weak transcription	NHEK	skin
31	chr9:98686400-98694600	Weak transcription	Primary B cells from peripheral blood	blood
32	chr9:98686400-98695200	Weak transcription	K562	blood
33	chr9:98686400-98702200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr9:98686400-98709000	Weak transcription	Right Ventricle	heart
35	chr9:98686400-98711000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr9:98686400-98743800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr9:98686800-98696800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr9:98687200-98695800	Weak transcription	Brain Germinal Matrix	brain
39	chr9:98687600-98694000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr9:98687800-98693600	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr9:98687800-98694400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr9:98687800-98694400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr9:98687800-98694400	Weak transcription	Fetal Intestine Large	intestine
44	chr9:98687800-98694400	Weak transcription	Fetal Intestine Small	intestine
45	chr9:98687800-98695400	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr9:98687800-98695800	Weak transcription	Thymus	Thymus
47	chr9:98687800-98697600	Weak transcription	Ovary	ovary
48	chr9:98687800-98700600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr9:98687800-98701800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr9:98687800-98703400	Weak transcription	Hela-S3	cervix

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