Variant report

Variant	rs4925138
Chromosome Location	chr17:17992793-17992794
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17991360..17993195-chr17:18000519..18002843,2	MCF-7	breast:
2	chr17:17991646..17993233-chr17:17995608..17997950,2	K562	blood:
3	chr17:17968674..17971093-chr17:17991115..17992806,2	K562	blood:
4	chr17:17984151..17987033-chr17:17992447..17995446,2	K562	blood:
5	chr17:17941361..17944192-chr17:17991166..17993409,5	K562	blood:
6	chr17:17989884..17994353-chr17:18008301..18011863,4	MCF-7	breast:
7	chr17:17991589..17993318-chr17:18013576..18015292,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171953	Chromatin interaction
ENSG00000108591	Chromatin interaction
ENSG00000141034	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11652894	0.87[ASN][1000 genomes]
rs12943202	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12943914	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12948749	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12949525	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12952818	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2230316	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2955351	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2955360	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2955371	0.86[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2955382	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4244602	0.82[JPT][hapmap]
rs4341796	0.82[JPT][hapmap];0.84[MEX][hapmap]
rs4925129	0.82[JPT][hapmap];0.84[MEX][hapmap]
rs4925130	0.82[JPT][hapmap];0.80[MEX][hapmap]
rs5002487	0.82[JPT][hapmap];0.84[MEX][hapmap]
rs6502625	0.83[CEU][hapmap];0.82[JPT][hapmap]
rs6502629	0.87[CEU][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap]
rs712265	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7207395	0.82[JPT][hapmap]
rs7222480	0.84[MEX][hapmap]
rs7224815	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs72827413	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8070128	0.82[JPT][hapmap];0.84[MEX][hapmap]
rs8078138	0.82[JPT][hapmap];0.84[MEX][hapmap]
rs8078583	0.82[JPT][hapmap]
rs8079418	0.82[AMR][1000 genomes]
rs8080823	0.82[JPT][hapmap];0.84[MEX][hapmap]
rs854762	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs854764	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs854765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs854766	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs854810	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs854813	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
4	nsv960429	chr17:17951047-18027679	Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv482491	chr17:17959577-18153920	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv1061162	chr17:17978838-18259234	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv492305	chr17:17980441-18424702	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4925138	SREBF1	cis	Whole Blood	GTEx
rs4925138	DRG2	cis	Thyroid	GTEx
rs4925138	TOM1L2	cis	parietal	SCAN
rs4925138	TOM1L2	cis	cerebellum	SCAN
rs4925138	C17orf39	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17990800-17992800	Active TSS	GM12878-XiMat	blood
2	chr17:17991600-17993000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr17:17991800-17997000	Weak transcription	Aorta	Aorta
4	chr17:17991800-18009800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr17:17992000-17992800	Enhancers	Lung	lung
6	chr17:17992000-17993000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr17:17992000-17993000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
8	chr17:17992000-17993000	Enhancers	Gastric	stomach
9	chr17:17992000-17993200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr17:17992000-17993200	Enhancers	Primary B cells from peripheral blood	blood
11	chr17:17992000-17993400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr17:17992000-18000600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr17:17992200-17992800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr17:17992200-17992800	Enhancers	Placenta	Placenta
15	chr17:17992200-17992800	Weak transcription	Small Intestine	intestine
16	chr17:17992200-17993200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr17:17992200-17993200	Weak transcription	Fetal Stomach	stomach
18	chr17:17992200-17993400	Enhancers	Primary T cells fromperipheralblood	blood
19	chr17:17992200-17993400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr17:17992200-17993600	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr17:17992200-17994200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr17:17992200-17997000	Weak transcription	Fetal Heart	heart
23	chr17:17992200-18000800	Weak transcription	Psoas Muscle	Psoas
24	chr17:17992200-18002400	Weak transcription	Fetal Brain Male	brain
25	chr17:17992200-18014000	Weak transcription	Right Atrium	heart
26	chr17:17992400-17992800	Enhancers	Muscle Satellite Cultured Cells	--
27	chr17:17992400-17992800	Enhancers	Dnd41	blood
28	chr17:17992400-17992800	Enhancers	HepG2	liver
29	chr17:17992400-17993000	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr17:17992400-17993000	Enhancers	Adipose Nuclei	Adipose
31	chr17:17992400-17993000	Enhancers	A549	lung
32	chr17:17992400-17993000	Enhancers	Hela-S3	cervix
33	chr17:17992400-17993000	Enhancers	K562	blood
34	chr17:17992400-17993200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr17:17992400-17993200	Enhancers	Stomach Smooth Muscle	stomach
36	chr17:17992400-17993400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr17:17992400-17993800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr17:17992400-17994000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr17:17992400-17994200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr17:17992400-17994200	Weak transcription	Primary T cells from cord blood	blood
41	chr17:17992400-17994200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr17:17992400-17994200	Weak transcription	Fetal Intestine Small	intestine
43	chr17:17992400-17994200	Weak transcription	Fetal Muscle Leg	muscle
44	chr17:17992400-17994400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr17:17992400-17994400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr17:17992400-17994400	Weak transcription	Fetal Thymus	thymus
47	chr17:17992400-17994400	Weak transcription	Rectal Smooth Muscle	rectum
48	chr17:17992400-17994600	Weak transcription	Thymus	Thymus
49	chr17:17992400-17994800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr17:17992400-17994800	Weak transcription	Liver	Liver

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