Variant report

Variant	rs6479420
Chromosome Location	chr9:95116406-95116407
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	chr9:95114363..95116588-chr9:95118609..95121490,2	K562	blood:

Extended variants
information (count: 119 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10115222	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10115290	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10116241	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10117627	0.91[ASN][1000 genomes]
rs10120980	0.85[EUR][1000 genomes]
rs10121495	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10123342	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10123738	0.81[AMR][1000 genomes]
rs10125474	0.85[EUR][1000 genomes]
rs10283572	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10429459	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10453241	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10514815	0.90[ASN][1000 genomes]
rs1053441	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1053446	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10739927	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10739928	0.86[EUR][1000 genomes]
rs10761147	0.84[EUR][1000 genomes]
rs10761150	0.85[EUR][1000 genomes]
rs10761151	0.85[EUR][1000 genomes]
rs10761153	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10761154	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10761158	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10761161	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10820960	0.85[EUR][1000 genomes]
rs10820961	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10820964	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10820965	0.86[EUR][1000 genomes]
rs10820966	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10820967	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10820969	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10820971	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10820990	0.81[AMR][1000 genomes]
rs10992273	0.83[EUR][1000 genomes]
rs10992280	0.85[EUR][1000 genomes]
rs10992291	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10992303	0.86[EUR][1000 genomes]
rs10992319	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10992322	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10992340	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10992347	0.92[ASN][1000 genomes]
rs1121979	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1133908	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11789163	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11792342	0.84[EUR][1000 genomes]
rs11795122	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12335553	0.82[AMR][1000 genomes]
rs12343820	0.91[ASN][1000 genomes]
rs12348488	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12353096	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1535754	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1924243	0.92[ASN][1000 genomes]
rs1924244	0.91[ASN][1000 genomes]
rs2007837	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2025388	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2151618	0.82[EUR][1000 genomes]
rs2236341	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2273862	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2274966	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2295941	0.85[EUR][1000 genomes]
rs2296666	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2296667	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2516567	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2516568	0.82[EUR][1000 genomes]
rs2761679	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2761681	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3118008	0.94[ASN][1000 genomes]
rs3739606	0.91[ASN][1000 genomes]
rs3758229	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs3780347	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4302908	0.81[AMR][1000 genomes]
rs4744133	0.92[ASN][1000 genomes]
rs4744134	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4744135	0.90[ASN][1000 genomes]
rs4744136	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6479416	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6479417	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6479418	0.86[EUR][1000 genomes]
rs6479419	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479423	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7020874	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7023004	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7024190	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7026361	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7027595	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7031567	0.90[ASN][1000 genomes]
rs7040949	0.83[EUR][1000 genomes]
rs7042335	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7043152	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7045409	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7047089	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs710162	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7847929	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7848055	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7850432	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7852510	0.81[AMR][1000 genomes]
rs7853859	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7856204	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7860774	0.86[ASN][1000 genomes]
rs7860786	0.87[ASN][1000 genomes]
rs7863234	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7863406	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7864630	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7867909	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7868640	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7869742	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7872375	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7873932	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8067	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs927865	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9299403	0.85[EUR][1000 genomes]
rs9299404	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs987554	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv893573	chr9:94974188-95355719	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv1045165	chr9:95057462-95138564	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv1047337	chr9:95105638-95347484	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6479420	NOL8	Cis_1M	lymphoblastoid	RTeQTL
rs6479420	OGN	cis	Nerve Tibial	GTEx

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95089600-95121800	Weak transcription	Fetal Heart	heart
2	chr9:95090400-95118200	Weak transcription	HepG2	liver
3	chr9:95091000-95120000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr9:95100800-95116600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr9:95101600-95116600	Weak transcription	Brain Substantia Nigra	brain
6	chr9:95102000-95116600	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr9:95102000-95121000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr9:95102200-95117600	Weak transcription	Fetal Brain Female	brain
9	chr9:95102200-95121400	Weak transcription	A549	lung
10	chr9:95102600-95116600	Weak transcription	Thymus	Thymus
11	chr9:95102600-95120800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr9:95104200-95118000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr9:95104200-95119800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr9:95104200-95121200	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr9:95113400-95116600	Weak transcription	NHLF	lung
16	chr9:95113400-95117000	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr9:95113400-95119400	Weak transcription	Fetal Lung	lung
18	chr9:95113400-95121800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr9:95113600-95116600	Weak transcription	NHDF-Ad	bronchial
20	chr9:95113600-95117800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr9:95114200-95116600	Weak transcription	Ovary	ovary
22	chr9:95114200-95117000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr9:95115000-95116600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr9:95115600-95116600	Strong transcription	Fetal Muscle Leg	muscle
25	chr9:95115600-95116800	ZNF genes & repeats	Dnd41	blood
26	chr9:95115800-95117000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr9:95115800-95117000	Weak transcription	Duodenum Mucosa	Duodenum
28	chr9:95116000-95116600	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr9:95116000-95116800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
30	chr9:95116000-95116800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr9:95116000-95118000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
32	chr9:95116200-95116800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr9:95116200-95116800	Strong transcription	Primary T cells from cord blood	blood
34	chr9:95116200-95116800	Strong transcription	Primary hematopoietic stem cells	blood
35	chr9:95116200-95117000	ZNF genes & repeats	Aorta	Aorta
36	chr9:95116200-95117600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
37	chr9:95116400-95116600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr9:95116400-95116800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
39	chr9:95116400-95116800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr9:95116400-95116800	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr9:95116400-95116800	ZNF genes & repeats	Fetal Muscle Trunk	muscle
42	chr9:95116400-95116800	ZNF genes & repeats	Lung	lung
43	chr9:95116400-95116800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
44	chr9:95116400-95117000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr9:95116400-95118000	Weak transcription	Fetal Thymus	thymus
46	chr9:95116400-95118800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links