Variant report

Variant	rs10495882
Chromosome Location	chr2:39227392-39227393
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 99 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10166557	1.00[EUR][1000 genomes]
rs10173380	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10173563	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10184046	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10184855	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10186842	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10188701	1.00[EUR][1000 genomes]
rs10189440	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10194533	1.00[EUR][1000 genomes]
rs10196863	1.00[EUR][1000 genomes]
rs10199955	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10202876	1.00[EUR][1000 genomes]
rs10203565	1.00[EUR][1000 genomes]
rs10207187	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10207984	1.00[EUR][1000 genomes]
rs1059313	1.00[ASN][1000 genomes]
rs12329307	1.00[EUR][1000 genomes]
rs13387231	1.00[EUR][1000 genomes]
rs13394446	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs13395448	1.00[EUR][1000 genomes]
rs13407659	1.00[EUR][1000 genomes]
rs13411756	1.00[CEU][hapmap];0.87[YRI][hapmap];1.00[EUR][1000 genomes]
rs13416725	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs13424493	1.00[EUR][1000 genomes]
rs13425165	1.00[EUR][1000 genomes]
rs13428418	1.00[EUR][1000 genomes]
rs13432395	1.00[EUR][1000 genomes]
rs1451278	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17023148	1.00[EUR][1000 genomes]
rs17023149	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17023214	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17023241	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17023292	1.00[CEU][hapmap];0.93[YRI][hapmap];1.00[EUR][1000 genomes]
rs17425982	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1901290	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2218850	1.00[EUR][1000 genomes]
rs2373466	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2373472	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs3099938	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs3099947	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs3099953	1.00[EUR][1000 genomes]
rs3099973	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs3099986	1.00[EUR][1000 genomes]
rs3099996	1.00[EUR][1000 genomes]
rs3099997	1.00[EUR][1000 genomes]
rs3112138	1.00[JPT][hapmap]
rs3112145	1.00[EUR][1000 genomes]
rs3112146	1.00[EUR][1000 genomes]
rs3112148	1.00[EUR][1000 genomes]
rs3112155	1.00[EUR][1000 genomes]
rs3112157	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs3112158	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs3112160	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs3112164	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs3112174	1.00[EUR][1000 genomes]
rs3112176	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs3112177	1.00[EUR][1000 genomes]
rs55890805	1.00[EUR][1000 genomes]
rs56269328	1.00[EUR][1000 genomes]
rs56724744	1.00[EUR][1000 genomes]
rs57359008	1.00[EUR][1000 genomes]
rs59259697	1.00[EUR][1000 genomes]
rs60703378	1.00[EUR][1000 genomes]
rs61596046	1.00[EUR][1000 genomes]
rs6544182	1.00[JPT][hapmap]
rs6544200	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6722478	1.00[JPT][hapmap]
rs6734212	1.00[EUR][1000 genomes]
rs6737680	1.00[EUR][1000 genomes]
rs6748000	1.00[JPT][hapmap]
rs6751306	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6753426	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6754613	1.00[EUR][1000 genomes]
rs718312	1.00[EUR][1000 genomes]
rs72906436	1.00[EUR][1000 genomes]
rs72906467	1.00[EUR][1000 genomes]
rs72916836	1.00[EUR][1000 genomes]
rs72916860	1.00[EUR][1000 genomes]
rs72918710	1.00[EUR][1000 genomes]
rs72925431	1.00[EUR][1000 genomes]
rs72925433	1.00[EUR][1000 genomes]
rs72925439	1.00[EUR][1000 genomes]
rs7340303	1.00[EUR][1000 genomes]
rs73930506	1.00[EUR][1000 genomes]
rs7559586	1.00[EUR][1000 genomes]
rs7564481	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7565814	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7571608	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7571719	1.00[CEU][hapmap];0.93[YRI][hapmap];1.00[EUR][1000 genomes]
rs7574214	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7582586	1.00[EUR][1000 genomes]
rs7583010	1.00[CEU][hapmap]
rs7589303	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7599990	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9646968	1.00[EUR][1000 genomes]
rs9678084	1.00[CEU][hapmap];0.87[YRI][hapmap]

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	nsv873884	chr2:39154463-39332093	Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv2755359	chr2:39169049-39417849	Strong transcription Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv873885	chr2:39200198-39573521	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10495882	SOS1	cis	multi-tissue	Pritchard

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39200800-39227800	Weak transcription	Fetal Heart	heart
2	chr2:39202400-39228800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr2:39205800-39242600	Weak transcription	Psoas Muscle	Psoas
4	chr2:39206000-39235800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:39210000-39232000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:39210400-39233200	Strong transcription	Rectal Mucosa Donor 29	rectum
7	chr2:39210400-39241600	Strong transcription	Adipose Nuclei	Adipose
8	chr2:39210400-39242600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr2:39210600-39229400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:39210600-39242400	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr2:39210800-39230200	Strong transcription	Dnd41	blood
12	chr2:39211000-39247600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr2:39211200-39228600	Strong transcription	HepG2	liver
14	chr2:39211400-39237800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr2:39211600-39242000	Weak transcription	Stomach Mucosa	stomach
16	chr2:39211800-39231200	Strong transcription	Rectal Mucosa Donor 31	rectum
17	chr2:39211800-39239600	Strong transcription	Fetal Intestine Large	intestine
18	chr2:39213400-39228000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:39213400-39228800	Weak transcription	Brain Angular Gyrus	brain
20	chr2:39213400-39234400	Weak transcription	Gastric	stomach
21	chr2:39213400-39234400	Weak transcription	NHEK	skin
22	chr2:39213400-39242200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:39213400-39242600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:39213400-39251200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr2:39213400-39259800	Weak transcription	Right Ventricle	heart
26	chr2:39213800-39228200	Weak transcription	Fetal Intestine Small	intestine
27	chr2:39213800-39235000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr2:39213800-39235000	Weak transcription	Small Intestine	intestine
29	chr2:39213800-39308000	Weak transcription	Pancreas	Pancrea
30	chr2:39214200-39235400	Weak transcription	Hela-S3	cervix
31	chr2:39217400-39229000	Strong transcription	Liver	Liver
32	chr2:39217400-39241800	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr2:39217600-39230200	Strong transcription	Primary T cells from cord blood	blood
34	chr2:39217600-39231200	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr2:39217600-39234200	Strong transcription	Primary B cells from peripheral blood	blood
36	chr2:39217600-39242400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr2:39217600-39244200	Strong transcription	Primary B cells from cord blood	blood
38	chr2:39218800-39241200	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr2:39219000-39259200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr2:39219200-39244000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr2:39219400-39228200	Weak transcription	Ovary	ovary
42	chr2:39219400-39242600	Weak transcription	Brain Substantia Nigra	brain
43	chr2:39220400-39233000	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr2:39220600-39237000	Strong transcription	Fetal Thymus	thymus
45	chr2:39221000-39241200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr2:39221800-39228600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr2:39222600-39227400	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr2:39223400-39227600	Weak transcription	Colon Smooth Muscle	Colon
49	chr2:39223400-39230000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr2:39223600-39228200	Weak transcription	Fetal Stomach	stomach

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