Variant report

Variant	rs1999023
Chromosome Location	chr9:98748020-98748021
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:98746769..98748896-chr9:98754833..98756398,2	K562	blood:
2	chr9:98746100..98748264-chr9:98759830..98761515,2	MCF-7	breast:
3	chr9:98746263..98748269-chr9:98754898..98757748,2	K562	blood:
4	chr9:98719153..98720916-chr9:98745927..98748838,2	K562	blood:
5	chr9:98726229..98728206-chr9:98747751..98749981,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10983321	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs10988581	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10988792	0.81[ASW][hapmap];0.82[LWK][hapmap];0.90[MKK][hapmap];0.90[TSI][hapmap]
rs10988804	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.90[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11787559	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11790370	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11790491	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11793298	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11794054	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12001	0.89[GIH][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap]
rs12683634	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12685221	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12685807	0.89[GIH][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap]
rs12686222	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12686457	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1360064	0.90[CEU][hapmap];0.90[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16910262	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16910296	0.90[CEU][hapmap];0.90[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16910298	0.90[CEU][hapmap];0.90[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16910418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1831228	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2026032	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2069053	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2274654	0.81[ASW][hapmap];0.92[GIH][hapmap];0.95[MKK][hapmap];0.90[TSI][hapmap]
rs34533243	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3780574	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4532708	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4742775	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4742781	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4743372	0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4743417	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs4743418	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4743436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4743472	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7048414	0.90[CEU][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes]
rs73536517	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73656544	0.82[EUR][1000 genomes]
rs7868270	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1999023	C9orf130	Cis_1M	lymphoblastoid	RTeQTL
rs1999023	LINC00476	cis	Whole Blood	GTEx
rs1999023	LINC00476	cis	Esophagus Mucosa	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98706400-98777400	Weak transcription	Psoas Muscle	Psoas
2	chr9:98714000-98782600	Weak transcription	HUVEC	blood vessel
3	chr9:98719000-98751400	Weak transcription	Stomach Mucosa	stomach
4	chr9:98719200-98749600	Weak transcription	Fetal Intestine Small	intestine
5	chr9:98719200-98749800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr9:98719200-98752800	Weak transcription	Pancreas	Pancrea
7	chr9:98719200-98764200	Weak transcription	Spleen	Spleen
8	chr9:98719200-98767800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr9:98719400-98767200	Weak transcription	Right Ventricle	heart
10	chr9:98719400-98771000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr9:98719600-98766800	Weak transcription	Colon Smooth Muscle	Colon
12	chr9:98723800-98749800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr9:98726400-98767800	Weak transcription	Gastric	stomach
14	chr9:98730600-98751200	Weak transcription	Small Intestine	intestine
15	chr9:98732200-98751200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr9:98733000-98749600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr9:98734600-98749800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr9:98734600-98764400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr9:98734600-98767800	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr9:98734600-98782400	Weak transcription	NHEK	skin
21	chr9:98735200-98751600	Weak transcription	NHDF-Ad	bronchial
22	chr9:98735400-98778400	Weak transcription	Hela-S3	cervix
23	chr9:98735800-98748400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr9:98735800-98764200	Weak transcription	Placenta	Placenta
25	chr9:98735800-98766600	Weak transcription	Stomach Smooth Muscle	stomach
26	chr9:98735800-98770600	Weak transcription	K562	blood
27	chr9:98735800-98771200	Weak transcription	HepG2	liver
28	chr9:98736000-98749800	Weak transcription	Lung	lung
29	chr9:98736000-98751400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr9:98736200-98752800	Weak transcription	Fetal Muscle Trunk	muscle
31	chr9:98736400-98749200	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr9:98736400-98751000	Weak transcription	Ovary	ovary
33	chr9:98736600-98778800	Weak transcription	Fetal Brain Male	brain
34	chr9:98737000-98766800	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr9:98738800-98756400	Weak transcription	Aorta	Aorta
36	chr9:98741800-98778600	Weak transcription	NH-A	brain
37	chr9:98743200-98755800	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr9:98743400-98749600	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr9:98744600-98750000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr9:98744600-98768000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr9:98744800-98748600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr9:98744800-98748800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr9:98744800-98749800	Weak transcription	Fetal Brain Female	brain
44	chr9:98744800-98749800	Weak transcription	Fetal Muscle Leg	muscle
45	chr9:98744800-98749800	Weak transcription	Fetal Stomach	stomach
46	chr9:98744800-98749800	Weak transcription	Thymus	Thymus
47	chr9:98744800-98751600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr9:98744800-98752800	Weak transcription	Brain Anterior Caudate	brain
49	chr9:98744800-98753000	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr9:98744800-98753000	Weak transcription	Brain Substantia Nigra	brain

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