Variant report

Variant	rs2341479
Chromosome Location	chr1:161885352-161885353
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10733044	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10737502	0.90[ASN][1000 genomes]
rs10753645	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10753666	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10799979	0.81[YRI][hapmap]
rs10800068	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1394070	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1553444	0.94[ASN][1000 genomes]
rs16846343	0.84[YRI][hapmap]
rs16852678	0.84[YRI][hapmap]
rs1806594	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2055539	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2134690	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2134696	0.90[ASN][1000 genomes]
rs2298019	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2341468	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2499855	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2499856	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2880055	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34312480	1.00[ASN][1000 genomes]
rs34461550	0.90[ASN][1000 genomes]
rs35621393	0.94[ASN][1000 genomes]
rs36080602	1.00[ASN][1000 genomes]
rs3767633	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4233380	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4300199	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4579731	0.90[ASN][1000 genomes]
rs4656335	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4656339	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657103	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6427633	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427639	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6667896	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6685369	0.90[ASN][1000 genomes]
rs6698065	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6701754	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs71639910	0.98[ASN][1000 genomes]
rs7517386	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7532448	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs924777	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33393	chr1:161478681-162080327	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv464184	chr1:161646807-161885352	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv548075	chr1:161646807-161885352	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv464206	chr1:161798239-162067447	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv470744	chr1:161798239-162067447	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv548077	chr1:161798239-162067447	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer 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 miRNA target site	15 gene(s)	inside rSNPs	diseases
7	esv3440913	chr1:161864485-161897210	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv3353497	chr1:161864505-161897180	Enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2341479	OR10J1	cis	parietal	SCAN
rs2341479	PEA15	cis	parietal	SCAN
rs2341479	NUF2	cis	cerebellum	SCAN
rs2341479	TAGLN2	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161824200-161928400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr1:161836600-161888400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr1:161859200-161885400	Weak transcription	Psoas Muscle	Psoas
4	chr1:161861600-161891400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr1:161861600-161906400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr1:161861600-161936000	Weak transcription	Fetal Intestine Small	intestine
7	chr1:161875600-161888400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr1:161877400-161891400	Weak transcription	Colon Smooth Muscle	Colon
9	chr1:161878200-161888200	Weak transcription	Fetal Heart	heart
10	chr1:161879200-161886000	Weak transcription	Brain Angular Gyrus	brain
11	chr1:161879200-161886800	Weak transcription	Esophagus	oesophagus
12	chr1:161880000-161890600	Weak transcription	Fetal Muscle Trunk	muscle
13	chr1:161880000-161891600	Weak transcription	Fetal Stomach	stomach
14	chr1:161880400-161888400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr1:161880600-161888000	Weak transcription	Right Ventricle	heart
16	chr1:161880600-161890800	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr1:161880600-161892000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:161880800-161888400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr1:161880800-161891200	Weak transcription	Brain Hippocampus Middle	brain
20	chr1:161880800-161891200	Weak transcription	NHLF	lung
21	chr1:161881000-161886000	Strong transcription	Primary B cells from cord blood	blood
22	chr1:161881000-161887200	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr1:161881000-161890600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:161881400-161886000	Strong transcription	Primary B cells from peripheral blood	blood
25	chr1:161881400-161886000	Weak transcription	Hela-S3	cervix
26	chr1:161881600-161887200	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr1:161881600-161898800	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr1:161881600-161912000	Weak transcription	Aorta	Aorta
29	chr1:161881800-161887200	Strong transcription	Primary hematopoietic stem cells	blood
30	chr1:161881800-161887200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr1:161881800-161887200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr1:161881800-161890400	Weak transcription	HSMMtube	muscle
33	chr1:161882000-161886000	Strong transcription	Adipose Nuclei	Adipose
34	chr1:161882000-161887400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr1:161882000-161887800	Weak transcription	Spleen	Spleen
36	chr1:161882200-161888400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr1:161882200-161889400	Weak transcription	Brain Substantia Nigra	brain
38	chr1:161882400-161885400	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr1:161882400-161886000	Genic enhancers	Liver	Liver
40	chr1:161882400-161886000	Strong transcription	Placenta	Placenta
41	chr1:161882400-161887000	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr1:161882400-161887000	Strong transcription	Dnd41	blood
43	chr1:161882600-161885800	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr1:161882800-161885400	Enhancers	Osteobl	bone
45	chr1:161883000-161898600	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr1:161883200-161888400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr1:161883200-161916000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:161883400-161885600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr1:161883400-161886000	Strong transcription	K562	blood
50	chr1:161883400-161886400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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