Variant report

Variant	rs587000
Chromosome Location	chr1:228132290-228132291
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227916221..227923035-chr1:228131852..228141791,18	MCF-7	breast:
2	chr1:228131240..228133349-chr1:228272206..228274582,2	K562	blood:
3	chr1:227727960..227729815-chr1:228131832..228133962,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143740	Chromatin interaction
ENSG00000081692	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10916244	0.80[CEU][hapmap]
rs11584326	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1418422	0.91[EUR][1000 genomes]
rs1636193	0.93[EUR][1000 genomes]
rs1636194	0.94[EUR][1000 genomes]
rs1636195	1.00[ASW][hapmap];0.81[CEU][hapmap]
rs1636196	0.81[ASN][1000 genomes]
rs1745413	1.00[ASW][hapmap];0.81[CEU][hapmap]
rs1774754	0.93[EUR][1000 genomes]
rs2262292	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2485254	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527614	0.81[TSI][hapmap]
rs2527615	0.81[TSI][hapmap]
rs2796055	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2796056	0.81[TSI][hapmap]
rs3094911	0.81[CEU][hapmap]
rs592736	0.81[TSI][hapmap]
rs594916	0.81[TSI][hapmap]
rs596675	0.81[TSI][hapmap]
rs601050	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs632832	0.81[TSI][hapmap]
rs634106	0.81[TSI][hapmap]
rs638877	0.97[EUR][1000 genomes]
rs640440	0.94[EUR][1000 genomes]
rs652141	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs662658	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs680148	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs681824	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs697761	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs697763	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs708108	0.81[CEU][hapmap];0.85[CHB][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.84[TSI][hapmap]
rs708109	1.00[ASW][hapmap];0.81[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs708110	0.84[ASN][1000 genomes]
rs708118	0.81[CEU][hapmap]
rs708121	1.00[ASW][hapmap];0.81[CEU][hapmap];0.85[CHB][hapmap];0.80[CHD][hapmap];0.89[JPT][hapmap]
rs708123	0.81[CEU][hapmap]
rs708124	0.81[CEU][hapmap]
rs849900	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
5	nsv1005852	chr1:227957099-228148363	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv535319	chr1:227957099-228148363	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
7	nsv516409	chr1:228035131-228296745	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
9	nsv873251	chr1:228051234-228160911	Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs587000	SNAP47	cis	cerebellum	SCAN
rs587000	ACBD3	cis	cerebellum	SCAN
rs587000	GUK1	cis	parietal	SCAN
rs587000	NUP133	cis	parietal	SCAN
rs587000	WDR26	cis	cerebellum	SCAN
rs587000	TMEM63A	cis	cerebellum	SCAN
rs587000	PARP1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228107800-228134400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:228109800-228134000	Weak transcription	Right Atrium	heart
3	chr1:228118400-228133000	Weak transcription	Ovary	ovary
4	chr1:228121000-228132600	Weak transcription	Fetal Intestine Small	intestine
5	chr1:228123800-228132600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:228126200-228134400	Flanking Active TSS	Stomach Smooth Muscle	stomach
7	chr1:228126600-228133400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
8	chr1:228127000-228133600	Enhancers	Fetal Muscle Leg	muscle
9	chr1:228128000-228133400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:228128200-228132800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:228128400-228133600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:228129000-228132800	Weak transcription	HSMM	muscle
13	chr1:228129400-228134400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
14	chr1:228130200-228133000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:228130200-228133600	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr1:228130400-228133000	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr1:228130600-228132800	Weak transcription	HSMMtube	muscle
18	chr1:228130600-228134400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
19	chr1:228130800-228133800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:228131000-228133000	Flanking Active TSS	Fetal Heart	heart
21	chr1:228131400-228132800	Weak transcription	Fetal Intestine Large	intestine
22	chr1:228131400-228133600	Enhancers	Fetal Stomach	stomach
23	chr1:228131800-228132800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:228131800-228133800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr1:228131800-228133800	Weak transcription	Brain Angular Gyrus	brain
26	chr1:228131800-228134000	Enhancers	Fetal Lung	lung
27	chr1:228131800-228134200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr1:228132000-228132600	Enhancers	Psoas Muscle	Psoas
29	chr1:228132000-228132800	Enhancers	Hela-S3	cervix
30	chr1:228132000-228133800	Enhancers	Brain Cingulate Gyrus	brain
31	chr1:228132000-228134200	Enhancers	Right Ventricle	heart
32	chr1:228132000-228134400	Enhancers	Left Ventricle	heart
33	chr1:228132200-228132400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
34	chr1:228132200-228132400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr1:228132200-228132600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr1:228132200-228132600	Weak transcription	Gastric	stomach
37	chr1:228132200-228132800	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr1:228132200-228133000	Enhancers	HMEC	breast
39	chr1:228132200-228133200	Weak transcription	Brain Substantia Nigra	brain
40	chr1:228132200-228133200	Flanking Active TSS	Colon Smooth Muscle	Colon
41	chr1:228132200-228133200	Weak transcription	NHLF	lung
42	chr1:228132200-228133400	Weak transcription	Brain Hippocampus Middle	brain
43	chr1:228132200-228133600	Enhancers	Colonic Mucosa	Colon
44	chr1:228132200-228133600	Enhancers	Placenta Amnion	Placenta Amnion
45	chr1:228132200-228133800	Enhancers	Esophagus	oesophagus
46	chr1:228132200-228133800	Enhancers	Pancreas	Pancrea
47	chr1:228132200-228134000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr1:228132200-228134000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr1:228132200-228134200	Enhancers	Spleen	Spleen
50	chr1:228132200-228134400	Flanking Active TSS	Rectal Smooth Muscle	rectum

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