Variant report

Variant	rs2357231
Chromosome Location	chr1:210028454-210028455
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:210010076..210012426-chr1:210027665..210030061,2	K562	blood:
2	chr1:210021955..210024232-chr1:210027694..210029567,2	K562	blood:
3	chr1:210026504..210028571-chr1:210545991..210548661,2	K562	blood:
4	chr1:210026731..210029603-chr1:210060383..210062593,2	K562	blood:
5	chr1:210026504..210029493-chr1:210547161..210548663,2	K562	blood:

Variant related genes	Relation type
ENSG00000117597	Chromatin interaction
ENSG00000200972	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10863793	0.83[ASN][1000 genomes]
rs1108628	0.82[ASN][1000 genomes]
rs11119357	0.82[ASN][1000 genomes]
rs11579771	0.98[LWK][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs12022221	0.82[ASN][1000 genomes]
rs1883331	0.82[ASN][1000 genomes]
rs1963685	0.82[ASN][1000 genomes]
rs1964106	0.82[ASN][1000 genomes]
rs2049997	0.80[AFR][1000 genomes]
rs2049999	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2142907	0.82[ASN][1000 genomes]
rs4133950	0.82[ASN][1000 genomes]
rs4308980	0.82[ASN][1000 genomes]
rs4844497	0.80[AFR][1000 genomes]
rs583814	0.96[YRI][hapmap]
rs599663	0.84[LWK][hapmap];0.92[YRI][hapmap]
rs615276	0.96[YRI][hapmap]
rs661755	0.96[YRI][hapmap]
rs6689839	0.83[TSI][hapmap]
rs684083	0.84[LWK][hapmap];0.92[YRI][hapmap]
rs7537070	0.82[ASN][1000 genomes]
rs7537294	0.82[ASN][1000 genomes]
rs7540534	0.82[ASN][1000 genomes]
rs7542091	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7548545	0.82[ASN][1000 genomes]
rs7550330	0.82[ASN][1000 genomes]
rs7550733	0.82[ASN][1000 genomes]
rs9429825	0.80[ASN][1000 genomes]
rs9429826	0.80[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2357231	LPGAT1	cis	cerebellum	SCAN
rs2357231	TRAF3IP3	cis	lymphoblastoid	seeQTL
rs2357231	RCOR3	cis	parietal	SCAN
rs2357231	SYT14	cis	Nerve Tibial	GTEx
rs2357231	G0S2	cis	parietal	SCAN
rs2357231	HHAT	cis	cerebellum	SCAN
rs2357231	HHAT	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210001800-210034000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:210002400-210032000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:210003200-210028600	Strong transcription	Primary T cells fromperipheralblood	blood
4	chr1:210003200-210029400	Strong transcription	Fetal Muscle Trunk	muscle
5	chr1:210004000-210030800	Strong transcription	Primary B cells from cord blood	blood
6	chr1:210004200-210028800	Strong transcription	Adipose Nuclei	Adipose
7	chr1:210004200-210029600	Strong transcription	Fetal Muscle Leg	muscle
8	chr1:210004200-210030200	Strong transcription	Primary T cells from cord blood	blood
9	chr1:210004400-210029400	Strong transcription	Dnd41	blood
10	chr1:210013200-210028800	Strong transcription	Fetal Intestine Large	intestine
11	chr1:210013400-210028800	Strong transcription	Liver	Liver
12	chr1:210013800-210029400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr1:210014400-210028800	Strong transcription	NHEK	skin
14	chr1:210014400-210029400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:210017600-210041200	Weak transcription	Fetal Brain Male	brain
16	chr1:210018000-210032800	Weak transcription	Small Intestine	intestine
17	chr1:210018800-210029400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:210019000-210028600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr1:210019000-210033800	Weak transcription	Fetal Heart	heart
20	chr1:210019800-210028800	Strong transcription	Stomach Smooth Muscle	stomach
21	chr1:210019800-210030200	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr1:210020600-210029600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr1:210020800-210028800	Strong transcription	Skeletal Muscle Male	skeletal muscle
24	chr1:210022000-210029400	Strong transcription	Fetal Brain Female	brain
25	chr1:210022200-210029400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:210022200-210029400	Strong transcription	Thymus	Thymus
27	chr1:210022200-210029400	Strong transcription	Spleen	Spleen
28	chr1:210023000-210028600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
29	chr1:210023200-210029000	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr1:210023400-210029600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:210023800-210028800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:210024200-210030200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr1:210024400-210029200	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr1:210024400-210029400	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr1:210024400-210030000	Strong transcription	A549	lung
36	chr1:210024800-210029800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:210025000-210029000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr1:210025000-210029000	Strong transcription	Osteobl	bone
39	chr1:210025000-210035800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:210025200-210030200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr1:210025400-210029400	Strong transcription	Muscle Satellite Cultured Cells	--
42	chr1:210025600-210029600	Strong transcription	Lung	lung
43	chr1:210025800-210029400	Strong transcription	Fetal Intestine Small	intestine
44	chr1:210025800-210029600	Strong transcription	Fetal Stomach	stomach
45	chr1:210025800-210029600	Strong transcription	Ovary	ovary
46	chr1:210026200-210033200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr1:210026200-210035400	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr1:210026200-210035600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr1:210026400-210029000	Strong transcription	Esophagus	oesophagus
50	chr1:210026400-210029400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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