Variant report

Variant	rs10799319
Chromosome Location	chr1:225703485-225703486
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10753406	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10799311	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10799313	0.83[ASN][1000 genomes]
rs10799314	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10799316	0.81[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs10799317	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10799318	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10915828	0.81[CEU][hapmap];0.93[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.89[YRI][hapmap]
rs10915830	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10915833	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10915834	0.95[EUR][1000 genomes]
rs10915835	0.83[ASN][1000 genomes]
rs10915837	0.85[ASN][1000 genomes]
rs10915838	0.81[ASN][1000 genomes]
rs10915839	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10915847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11584675	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12028305	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1222440	1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.84[TSI][hapmap];0.83[ASN][1000 genomes]
rs12729655	0.85[ASN][1000 genomes]
rs2639703	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2639712	0.84[LWK][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap]
rs2639716	0.82[EUR][1000 genomes]
rs2657564	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2657569	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs2840958	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2840967	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs2840968	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs3820226	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3856156	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4653643	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs476540	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs487591	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs498350	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs510293	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs511649	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs516249	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs551996	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs554744	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs554992	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs561656	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs576861	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6426076	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6426078	0.83[ASN][1000 genomes]
rs6668770	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6676201	0.85[ASN][1000 genomes]
rs6678806	0.84[ASN][1000 genomes]
rs6697783	0.80[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap]
rs6702555	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6751	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs712062	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7515907	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7515963	0.85[ASN][1000 genomes]
rs7524766	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7540181	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7541598	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7555139	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7555553	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs812523	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs947034	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9804142	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][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	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	esv2756886	chr1:225665694-225703485	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	esv2759003	chr1:225665694-225703485	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv4720	chr1:225673218-225718009	Genic enhancers Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10799319	MRPL35	trans	brain	seeQTL
rs10799319	SEPT10	trans	brain	seeQTL
rs10799319	USP10	trans	brain	seeQTL
rs10799319	RP11-496N12.9	cis	Thyroid	GTEx
rs10799319	LBR	cis	Artery Tibial	GTEx
rs10799319	ZNF398	trans	brain	seeQTL
rs10799319	ENAH	cis	normal skin	skin_eQTL
rs10799319	C1orf109	trans	brain	seeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225677200-225703600	Weak transcription	Fetal Brain Female	brain
2	chr1:225687000-225705000	Weak transcription	Spleen	Spleen
3	chr1:225687400-225704400	Weak transcription	Fetal Stomach	stomach
4	chr1:225688600-225704600	Weak transcription	Placenta	Placenta
5	chr1:225688800-225711400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr1:225689200-225721000	Weak transcription	Duodenum Mucosa	Duodenum
7	chr1:225691000-225706200	Weak transcription	Primary B cells from cord blood	blood
8	chr1:225691200-225705000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:225692600-225704800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:225695400-225704800	Weak transcription	Fetal Brain Male	brain
11	chr1:225695600-225721200	Weak transcription	Fetal Kidney	kidney
12	chr1:225696600-225705000	Weak transcription	Gastric	stomach
13	chr1:225696800-225704800	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr1:225697200-225704800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:225697200-225704800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:225697200-225704800	Weak transcription	Pancreas	Pancrea
17	chr1:225697200-225705000	Weak transcription	Esophagus	oesophagus
18	chr1:225697200-225705000	Weak transcription	Lung	lung
19	chr1:225697200-225705400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:225697200-225711200	Weak transcription	Fetal Heart	heart
21	chr1:225697200-225716600	Weak transcription	Right Atrium	heart
22	chr1:225697400-225705000	Weak transcription	Aorta	Aorta
23	chr1:225697400-225705000	Weak transcription	Right Ventricle	heart
24	chr1:225697400-225715400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr1:225697400-225722600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr1:225697600-225703800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr1:225697800-225703800	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr1:225697800-225704800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:225697800-225705400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr1:225697800-225705400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr1:225697800-225706200	Weak transcription	Psoas Muscle	Psoas
32	chr1:225697800-225706800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:225697800-225707800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr1:225697800-225708600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr1:225698200-225705000	Weak transcription	NHEK	skin
36	chr1:225698600-225721000	Weak transcription	Small Intestine	intestine
37	chr1:225700000-225703800	Weak transcription	Fetal Muscle Leg	muscle
38	chr1:225700000-225704000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr1:225700000-225704600	Weak transcription	NHLF	lung
40	chr1:225700000-225705000	Weak transcription	Left Ventricle	heart
41	chr1:225700000-225726400	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr1:225700000-225726400	Weak transcription	HMEC	breast
43	chr1:225700200-225703800	Weak transcription	Stomach Smooth Muscle	stomach
44	chr1:225700400-225704600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr1:225700400-225708400	Weak transcription	Dnd41	blood
46	chr1:225700600-225704800	Weak transcription	HSMMtube	muscle
47	chr1:225700600-225706800	Weak transcription	Brain Germinal Matrix	brain
48	chr1:225700800-225703800	Weak transcription	Fetal Intestine Large	intestine
49	chr1:225700800-225704800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:225700800-225707000	Weak transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links