Variant report

Variant	rs2274654
Chromosome Location	chr9:98691137-98691138
allele	A/G
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:
2	chr9:98682356..98686313-chr9:98688317..98691201,4	K562	blood:

Variant related genes	Relation type
ENSG00000175611	Chromatin interaction
ENSG00000182150	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10988581	0.82[EUR][1000 genomes]
rs10988792	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10988804	0.90[ASW][hapmap];0.92[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];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];0.91[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12683310	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12685318	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12685807	0.92[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1360064	0.86[GIH][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap]
rs16910296	0.86[GIH][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap]
rs16910298	0.89[GIH][hapmap];0.93[MKK][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs1999023	0.81[ASW][hapmap];0.92[GIH][hapmap];0.95[MKK][hapmap];0.90[TSI][hapmap]
rs2026032	0.89[YRI][hapmap];0.99[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2069053	0.81[ASW][hapmap];0.89[GIH][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs2274653	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];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4742775	0.81[ASW][hapmap];0.86[GIH][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap]
rs4742781	0.81[ASW][hapmap];0.89[GIH][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap]
rs4743391	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743400	0.83[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743417	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[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];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs591486	0.81[YRI][hapmap]
rs7048414	0.83[GIH][hapmap];0.82[MKK][hapmap];0.90[TSI][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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2274654	C9orf130	cis	parietal	SCAN
rs2274654	HABP4	cis	cerebellum	SCAN
rs2274654	C9orf130	Cis_1M	lymphoblastoid	RTeQTL
rs2274654	OGN	cis	parietal	SCAN
rs2274654	AUH	cis	parietal	SCAN
rs2274654	LINC00476	cis	Esophagus Mucosa	GTEx
rs2274654	C9orf130	cis	lesional skin	skin_eQTL
rs2274654	LINC00476	cis	Skin Sun Exposed Lower leg	GTEx
rs2274654	LINC00476	cis	Esophagus Muscularis	GTEx
rs2274654	OMD	cis	parietal	SCAN
rs2274654	LINC00476	cis	Whole Blood	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

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links