Variant report

Variant	rs2464526
Chromosome Location	chr4:89879663-89879664
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	chr4:89879550..89882970-chr4:89885286..89887934,3	K562	blood:

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10019862	1.00[ASN][1000 genomes]
rs10028121	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10033435	0.96[ASN][1000 genomes]
rs10033476	0.96[ASN][1000 genomes]
rs1246630	0.92[ASN][1000 genomes]
rs1246633	0.92[ASN][1000 genomes]
rs1246637	0.88[ASN][1000 genomes]
rs1246638	0.96[ASN][1000 genomes]
rs1246639	0.84[ASN][1000 genomes]
rs1246641	0.96[ASN][1000 genomes]
rs1272570	0.92[ASN][1000 genomes]
rs13106968	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs13148439	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1379934	1.00[CHB][hapmap]
rs1398938	1.00[CHD][hapmap]
rs1458552	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1458553	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1458555	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1533294	1.00[CHB][hapmap]
rs1708673	1.00[CHD][hapmap]
rs1903004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1903009	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2045516	0.96[ASN][1000 genomes]
rs2125410	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2446295	0.92[ASN][1000 genomes]
rs2446302	0.84[ASN][1000 genomes]
rs2446309	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2464521	0.92[ASN][1000 genomes]
rs2609254	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2609263	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2609266	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[ASN][1000 genomes]
rs2609274	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2609278	0.96[ASN][1000 genomes]
rs2609281	0.96[ASN][1000 genomes]
rs2609284	0.88[ASN][1000 genomes]
rs2670618	1.00[CHD][hapmap]
rs2670619	1.00[CHB][hapmap]
rs2704572	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2704588	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2704591	0.96[ASN][1000 genomes]
rs2704592	1.00[CHD][hapmap]
rs2704593	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2704602	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2704603	0.96[ASN][1000 genomes]
rs2704606	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs28624770	1.00[ASN][1000 genomes]
rs28658282	1.00[ASN][1000 genomes]
rs2869965	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2869968	0.96[ASN][1000 genomes]
rs4498109	0.84[ASN][1000 genomes]
rs59698155	1.00[ASN][1000 genomes]
rs7673427	0.92[ASN][1000 genomes]
rs7697878	0.92[ASN][1000 genomes]
rs922027	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs973680	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs987314	1.00[ASW][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs993358	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009354	chr4:89725914-89985155	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv998651	chr4:89800245-89933445	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv537175	chr4:89800245-89933445	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv879532	chr4:89811195-89917135	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv879533	chr4:89832532-89917135	ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
7	nsv1007025	chr4:89837734-90098046	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv537176	chr4:89837734-90098046	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	esv1829430	chr4:89853598-89908308	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2464526	SPARCL1	cis	parietal	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:89851400-89883600	Weak transcription	Fetal Intestine Large	intestine
2	chr4:89852400-89885000	Weak transcription	Fetal Lung	lung
3	chr4:89864400-89881400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr4:89871000-89888600	Weak transcription	Small Intestine	intestine
5	chr4:89873000-89886000	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr4:89875200-89882000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr4:89875600-89880200	Enhancers	Placenta	Placenta
8	chr4:89877000-89889000	Weak transcription	Gastric	stomach
9	chr4:89877800-89880600	ZNF genes & repeats	Fetal Intestine Small	intestine
10	chr4:89877800-89882000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr4:89877800-89885600	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr4:89878000-89882400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr4:89878200-89880200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr4:89878400-89882400	Enhancers	Adipose Nuclei	Adipose
15	chr4:89878400-89927600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr4:89878600-89879800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr4:89878600-89879800	Enhancers	Duodenum Mucosa	Duodenum
18	chr4:89878600-89880000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr4:89878600-89888600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr4:89878800-89879800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr4:89879000-89880000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr4:89879000-89881600	Enhancers	Primary B cells from cord blood	blood
23	chr4:89879200-89880000	ZNF genes & repeats	Fetal Stomach	stomach
24	chr4:89879200-89880800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr4:89879400-89879800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr4:89879400-89879800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr4:89879400-89879800	Enhancers	Colonic Mucosa	Colon
28	chr4:89879400-89879800	Enhancers	Fetal Muscle Trunk	muscle
29	chr4:89879400-89880000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr4:89879400-89880000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr4:89879400-89880000	Enhancers	Colon Smooth Muscle	Colon
32	chr4:89879400-89880000	Enhancers	Left Ventricle	heart
33	chr4:89879400-89880000	Enhancers	Lung	lung
34	chr4:89879400-89880000	Enhancers	Pancreas	Pancrea
35	chr4:89879400-89880000	Enhancers	Right Atrium	heart
36	chr4:89879400-89880200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
37	chr4:89879400-89880600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr4:89879400-89880800	Enhancers	Spleen	Spleen
39	chr4:89879400-89884800	Weak transcription	Osteobl	bone
40	chr4:89879600-89879800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
41	chr4:89879600-89879800	Strong transcription	Ovary	ovary
42	chr4:89879600-89880000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr4:89879600-89880600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr4:89879600-89881600	Weak transcription	NHDF-Ad	bronchial
45	chr4:89879600-89883400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr4:89879600-89883600	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr4:89879600-89885800	Weak transcription	Esophagus	oesophagus
48	chr4:89879600-89888800	Weak transcription	Psoas Muscle	Psoas
49	chr4:89879600-89894000	Weak transcription	Primary hematopoietic stem cells	blood
50	chr4:89879600-89911200	Weak transcription	K562	blood

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