Variant report

Variant	rs6587557
Chromosome Location	chr1:151137144-151137145
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr1:151137076-151139334	K562	blood:	n/a	chr1:151137861-151137870

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:150979239..150982026-chr1:151136822..151140051,3	MCF-7	breast:
2	chr1:151017642..151020624-chr1:151136290..151137800,2	MCF-7	breast:
3	chr1:150550605..150553329-chr1:151136705..151138908,2	K562	blood:
4	chr1:151124206..151127003-chr1:151136189..151137837,2	MCF-7	breast:
5	chr1:150983476..150986465-chr1:151136618..151138245,2	MCF-7	breast:
6	chr1:151131080..151134028-chr1:151135601..151138206,6	K562	blood:
7	chr1:151136716..151140911-chr1:151168778..151172657,5	MCF-7	breast:
8	chr1:151040998..151044328-chr1:151135769..151140484,5	MCF-7	breast:
9	chr1:151029301..151033715-chr1:151136820..151141213,5	MCF-7	breast:
10	chr1:151136857..151140256-chr1:151168802..151172321,4	MCF-7	breast:
11	chr1:151020969..151022652-chr1:151136172..151138973,3	MCF-7	breast:
12	chr1:151136893..151140335-chr1:151160848..151164031,6	MCF-7	breast:
13	chr1:151117625..151120818-chr1:151135402..151140051,4	MCF-7	breast:
14	chr1:151136474..151139051-chr1:151252702..151254478,3	MCF-7	breast:
15	chr1:151127620..151129314-chr1:151136293..151138330,2	K562	blood:
16	chr1:150979986..150982538-chr1:151136841..151139170,3	K562	blood:
17	chr1:151029387..151032698-chr1:151136625..151139017,3	K562	blood:
18	chr1:151042255..151044217-chr1:151136884..151138558,2	MCF-7	breast:
19	chr1:151044680..151046429-chr1:151136336..151137837,2	K562	blood:
20	chr1:151106097..151107684-chr1:151136573..151139445,2	MCF-7	breast:

No data

Variant related genes	Relation type
SCNM1	TF binding region
ENSG00000163154	Chromatin interaction
ENSG00000143398	Chromatin interaction
ENSG00000163141	Chromatin interaction
ENSG00000197622	Chromatin interaction
ENSG00000213190	Chromatin interaction
ENSG00000143363	Chromatin interaction
ENSG00000143373	Chromatin interaction
ENSG00000163159	Chromatin interaction
ENSG00000232671	Chromatin interaction
ENSG00000143434	Chromatin interaction
ENSG00000163156	Chromatin interaction
ENSG00000143458	Chromatin interaction
ENSG00000143443	Chromatin interaction
ENSG00000143409	Chromatin interaction
ENSG00000143384	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10788798	0.86[JPT][hapmap]
rs11204777	0.86[JPT][hapmap]
rs11204780	0.86[JPT][hapmap]
rs11204782	0.85[JPT][hapmap]
rs11807526	0.86[JPT][hapmap]
rs12087892	0.86[JPT][hapmap]
rs1524773	0.85[JPT][hapmap]
rs2067606	0.86[JPT][hapmap]
rs2140709	0.86[JPT][hapmap]
rs3738481	0.85[JPT][hapmap]
rs4970993	0.86[JPT][hapmap]
rs4970998	0.86[JPT][hapmap]
rs4971005	0.86[JPT][hapmap]
rs4971007	0.86[JPT][hapmap]
rs4971008	0.86[JPT][hapmap]
rs6676190	0.86[JPT][hapmap]
rs7523731	0.86[JPT][hapmap]
rs7554936	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
5	nsv831559	chr1:151109459-151239921	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
6	nsv831570	chr1:151129020-151281778	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers 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	106 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs6587557	LYSMD1	cis	cerebellar cortex	BrainEAC
rs6587557	LCE3D	cis	cerebellum	SCAN
rs6587557	LCE2D	cis	cerebellum	SCAN
rs6587557	LYSMD1	cis	brain	BrainEAC
rs6587557	SELENBP1	cis	cerebellum	SCAN
rs6587557	GABPB2	cis	cerebellum	SCAN
rs6587557	CDC42SE1	cis	lymphoblastoid	seeQTL
rs6587557	LYSMD1	cis	parietal	SCAN
rs6587557	LYSMD1	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151131600-151137400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:151133600-151137200	Weak transcription	Aorta	Aorta
3	chr1:151134200-151137200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:151134200-151137600	Weak transcription	Lung	lung
5	chr1:151134400-151137200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:151134400-151137200	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr1:151134400-151137200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:151134400-151137200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr1:151134400-151137400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:151134400-151137400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:151134400-151137400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr1:151134400-151137400	Weak transcription	Esophagus	oesophagus
13	chr1:151134400-151137400	Weak transcription	Pancreas	Pancrea
14	chr1:151134600-151137200	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr1:151134600-151137200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:151134600-151137200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr1:151134600-151137200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr1:151134600-151137200	Weak transcription	Thymus	Thymus
19	chr1:151134600-151137400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr1:151134600-151137400	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr1:151135200-151137600	Weak transcription	Primary B cells from cord blood	blood
22	chr1:151135200-151137600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr1:151135600-151137600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr1:151135800-151137400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr1:151136000-151137600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr1:151136000-151137800	Genic enhancers	Primary T cells fromperipheralblood	blood
27	chr1:151136200-151137200	Enhancers	Psoas Muscle	Psoas
28	chr1:151136400-151137200	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr1:151136400-151137400	Genic enhancers	Primary T cells from cord blood	blood
30	chr1:151136600-151137200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:151136600-151137200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:151136600-151137200	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr1:151136600-151137200	Enhancers	Brain Substantia Nigra	brain
34	chr1:151136600-151137200	Genic enhancers	Fetal Thymus	thymus
35	chr1:151136600-151137400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:151136600-151137400	Transcr. at gene 5' and 3'	Brain Dorsolateral Prefrontal Cortex	brain
37	chr1:151136600-151137800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr1:151136600-151138000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr1:151136800-151137200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr1:151136800-151137200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr1:151136800-151137200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr1:151136800-151137200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr1:151136800-151137200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:151136800-151137200	Enhancers	Adipose Nuclei	Adipose
45	chr1:151136800-151137200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr1:151136800-151137200	Enhancers	Fetal Intestine Large	intestine
47	chr1:151136800-151137200	Flanking Active TSS	Stomach Smooth Muscle	stomach
48	chr1:151136800-151137200	Enhancers	NHEK	skin
49	chr1:151136800-151137200	Flanking Active TSS	NHLF	lung
50	chr1:151136800-151137400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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