Variant report

Variant	rs599663
Chromosome Location	chr1:210003388-210003389
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:210002486..210004655-chr1:210015863..210018980,3	K562	blood:
2	chr1:210001362..210003899-chr1:210005802..210009709,4	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11579771	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2049997	0.83[AMR][1000 genomes]
rs2236906	0.91[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap]
rs2357231	0.84[LWK][hapmap];0.92[YRI][hapmap]
rs3753516	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4844497	0.83[AMR][1000 genomes]
rs583814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs585191	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs593543	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs596731	0.80[EUR][1000 genomes]
rs597673	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs599021	0.94[ASN][1000 genomes]
rs615276	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs623360	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs632305	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs648349	0.91[ASN][1000 genomes]
rs651141	0.88[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.94[ASN][1000 genomes]
rs661755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs684083	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs846808	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs861019	0.88[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs599663	IL10	cis	cerebellum	SCAN
rs599663	IRF6	cis	cerebellum	SCAN
rs599663	SYT14	cis	Nerve Tibial	GTEx
rs599663	LPGAT1	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210001800-210004200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:210001800-210010200	Weak transcription	Spleen	Spleen
3	chr1:210001800-210025000	Weak transcription	Stomach Mucosa	stomach
4	chr1:210001800-210034000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:210002000-210003600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr1:210002000-210003600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr1:210002000-210003600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr1:210002000-210003600	Enhancers	Liver	Liver
9	chr1:210002000-210003800	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr1:210002000-210004000	Weak transcription	Brain Hippocampus Middle	brain
11	chr1:210002000-210004000	Weak transcription	Fetal Thymus	thymus
12	chr1:210002000-210004200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr1:210002000-210004200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr1:210002000-210004200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:210002000-210004200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr1:210002000-210004200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:210002000-210004200	Weak transcription	Brain Anterior Caudate	brain
18	chr1:210002000-210004200	Weak transcription	Fetal Lung	lung
19	chr1:210002000-210004200	Weak transcription	Pancreas	Pancrea
20	chr1:210002000-210004200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr1:210002000-210004200	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr1:210002000-210004800	Weak transcription	Aorta	Aorta
23	chr1:210002000-210006000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:210002000-210006000	Weak transcription	Gastric	stomach
25	chr1:210002000-210006200	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr1:210002000-210006400	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr1:210002000-210006600	Weak transcription	Esophagus	oesophagus
28	chr1:210002000-210006600	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr1:210002000-210007000	Weak transcription	Colonic Mucosa	Colon
30	chr1:210002000-210007000	Weak transcription	Thymus	Thymus
31	chr1:210002000-210007200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:210002000-210011200	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr1:210002000-210015600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr1:210002000-210023800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr1:210002200-210003600	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr1:210002200-210003800	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr1:210002200-210004200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr1:210002200-210004200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr1:210002200-210005600	Weak transcription	Fetal Intestine Small	intestine
40	chr1:210002200-210006600	Weak transcription	Right Ventricle	heart
41	chr1:210002400-210003400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:210002400-210003400	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr1:210002400-210003400	Flanking Active TSS	Hela-S3	cervix
44	chr1:210002400-210003600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:210002400-210003800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr1:210002400-210003800	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr1:210002400-210003800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
48	chr1:210002400-210003800	Enhancers	Brain Germinal Matrix	brain
49	chr1:210002400-210004000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr1:210002400-210004200	Weak transcription	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links