Variant report

Variant	rs7573310
Chromosome Location	chr2:39225538-39225539
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39219746..39222120-chr2:39223877..39225648,2	K562	blood:

Variant related genes	Relation type
ENSG00000229692	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10153761	0.80[ASN][1000 genomes]
rs10166801	0.83[ASN][1000 genomes]
rs10172714	0.92[AMR][1000 genomes]
rs10183915	0.91[ASN][1000 genomes]
rs10186762	0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10192250	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10194374	0.80[ASN][1000 genomes]
rs10201980	0.96[AMR][1000 genomes]
rs10439459	0.82[ASN][1000 genomes]
rs10779924	0.86[AMR][1000 genomes]
rs11124659	0.83[ASN][1000 genomes]
rs11692687	0.80[ASN][1000 genomes]
rs13023273	0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1454221	0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1454222	0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1454223	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1454225	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1454226	0.80[ASN][1000 genomes]
rs1454227	0.83[ASN][1000 genomes]
rs1454228	0.82[ASN][1000 genomes]
rs1470915	0.81[ASN][1000 genomes]
rs1840281	0.81[ASN][1000 genomes]
rs1869513	0.89[AMR][1000 genomes]
rs1869514	0.83[AMR][1000 genomes]
rs1947432	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2123876	0.91[ASN][1000 genomes]
rs2123881	0.81[ASN][1000 genomes]
rs2168044	0.86[AMR][1000 genomes]
rs2278912	0.92[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2278913	0.96[AMR][1000 genomes]
rs2278914	0.92[AMR][1000 genomes]
rs2290445	0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2305516	0.96[AMR][1000 genomes]
rs2373474	0.83[ASN][1000 genomes]
rs2373495	0.83[ASN][1000 genomes]
rs2373496	0.83[ASN][1000 genomes]
rs2603145	0.84[AMR][1000 genomes]
rs371745	0.89[AMR][1000 genomes]
rs3765058	0.89[AMR][1000 genomes]
rs4142729	0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs422854	0.93[AMR][1000 genomes]
rs4643520	0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4670270	0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4670272	0.80[ASN][1000 genomes]
rs4670901	0.96[AMR][1000 genomes]
rs4670903	0.93[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6544183	0.93[AMR][1000 genomes]
rs6544184	0.96[AMR][1000 genomes]
rs6544187	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6544191	0.89[ASN][1000 genomes]
rs6704656	0.96[AMR][1000 genomes]
rs6713281	0.82[ASN][1000 genomes]
rs6716101	0.96[AMR][1000 genomes]
rs6725356	0.83[ASN][1000 genomes]
rs6725644	0.83[ASN][1000 genomes]
rs6752850	0.92[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6755527	0.92[AMR][1000 genomes]
rs6756184	0.83[ASN][1000 genomes]
rs7568552	0.92[ASN][1000 genomes]
rs7571052	0.92[AMR][1000 genomes]
rs7577088	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7594644	0.86[AMR][1000 genomes]
rs9309031	0.83[ASN][1000 genomes]
rs958412	0.83[AMR][1000 genomes]
rs963731	0.82[ASN][1000 genomes]
rs9679498	0.96[AMR][1000 genomes];0.91[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	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
rs7573310	SOS1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39197000-39225800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:39200800-39227800	Weak transcription	Fetal Heart	heart
3	chr2:39202400-39225600	Weak transcription	Brain Cingulate Gyrus	brain
4	chr2:39202400-39228800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr2:39205800-39242600	Weak transcription	Psoas Muscle	Psoas
6	chr2:39206000-39235800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr2:39210000-39232000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:39210400-39233200	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr2:39210400-39241600	Strong transcription	Adipose Nuclei	Adipose
10	chr2:39210400-39242600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr2:39210600-39229400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr2:39210600-39242400	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr2:39210800-39230200	Strong transcription	Dnd41	blood
14	chr2:39211000-39247600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr2:39211200-39228600	Strong transcription	HepG2	liver
16	chr2:39211400-39237800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr2:39211600-39242000	Weak transcription	Stomach Mucosa	stomach
18	chr2:39211800-39231200	Strong transcription	Rectal Mucosa Donor 31	rectum
19	chr2:39211800-39239600	Strong transcription	Fetal Intestine Large	intestine
20	chr2:39213400-39225600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr2:39213400-39225600	Weak transcription	Brain Anterior Caudate	brain
22	chr2:39213400-39225800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr2:39213400-39225800	Weak transcription	Fetal Brain Female	brain
24	chr2:39213400-39225800	Weak transcription	Spleen	Spleen
25	chr2:39213400-39226400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr2:39213400-39226800	Weak transcription	Aorta	Aorta
27	chr2:39213400-39228000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr2:39213400-39228800	Weak transcription	Brain Angular Gyrus	brain
29	chr2:39213400-39234400	Weak transcription	Gastric	stomach
30	chr2:39213400-39234400	Weak transcription	NHEK	skin
31	chr2:39213400-39242200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr2:39213400-39242600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:39213400-39251200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr2:39213400-39259800	Weak transcription	Right Ventricle	heart
35	chr2:39213800-39226200	Weak transcription	K562	blood
36	chr2:39213800-39228200	Weak transcription	Fetal Intestine Small	intestine
37	chr2:39213800-39235000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr2:39213800-39235000	Weak transcription	Small Intestine	intestine
39	chr2:39213800-39308000	Weak transcription	Pancreas	Pancrea
40	chr2:39214200-39235400	Weak transcription	Hela-S3	cervix
41	chr2:39214800-39225600	Weak transcription	HSMMtube	muscle
42	chr2:39217400-39229000	Strong transcription	Liver	Liver
43	chr2:39217400-39241800	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr2:39217600-39230200	Strong transcription	Primary T cells from cord blood	blood
45	chr2:39217600-39231200	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr2:39217600-39234200	Strong transcription	Primary B cells from peripheral blood	blood
47	chr2:39217600-39242400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr2:39217600-39244200	Strong transcription	Primary B cells from cord blood	blood
49	chr2:39218800-39241200	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr2:39219000-39225800	Weak transcription	Colonic Mucosa	Colon

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