Variant report

Variant	rs10027549
Chromosome Location	chr4:648709-648710
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:644808..646339-chr4:648173..650037,2	K562	blood:
2	chr4:646849..649113-chr4:654761..657491,3	K562	blood:

Variant related genes	Relation type
ENSG00000272927	Chromatin interaction
ENSG00000133256	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10030136	1.00[ASN][1000 genomes]
rs1135375	1.00[ASN][1000 genomes]
rs13119162	0.87[AFR][1000 genomes]
rs28407346	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28470912	1.00[ASN][1000 genomes]
rs28483373	0.97[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28488910	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28504161	0.80[AMR][1000 genomes]
rs28525003	1.00[ASN][1000 genomes]
rs28568555	1.00[ASN][1000 genomes]
rs28569875	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28573204	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28583078	1.00[ASN][1000 genomes]
rs28630797	1.00[ASN][1000 genomes]
rs28742266	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28742899	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3864130	1.00[ASN][1000 genomes]
rs3864131	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3891250	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4463020	1.00[ASN][1000 genomes]
rs4518182	1.00[ASN][1000 genomes]
rs58227539	1.00[ASN][1000 genomes]
rs60316402	1.00[ASN][1000 genomes]
rs71602496	1.00[ASN][1000 genomes]
rs73056602	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73058406	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7436737	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9985747	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9991613	1.00[ASN][1000 genomes]
rs9992641	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011715	chr4:43860-823487	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh 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	esv2830422	chr4:72247-681939	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv931097	chr4:72447-683874	Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv532702	chr4:72447-755236	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers 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 miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv1005224	chr4:507005-900281	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Strong transcription Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv536976	chr4:507005-900281	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
7	nsv878245	chr4:509178-694613	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv822425	chr4:540105-1413799	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
9	nsv878246	chr4:592507-696848	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	esv2757916	chr4:603208-931354	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
11	esv2759217	chr4:603208-931354	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
12	nsv878247	chr4:607202-925149	Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
13	nsv530490	chr4:614355-1399150	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
14	nsv593206	chr4:625962-735150	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
15	nsv4194	chr4:635316-657212	Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv878248	chr4:645300-685993	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10027549	RP11-1191J2.2	cis	Thyroid	GTEx
rs10027549	RP11-1191J2.2	cis	Nerve Tibial	GTEx
rs10027549	RP11-1191J2.2	cis	lung	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:631400-657000	Weak transcription	Right Atrium	heart
2	chr4:641800-657000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:642200-652800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr4:642400-654600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr4:642800-657000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:643000-657000	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr4:645800-649400	Weak transcription	Pancreas	Pancrea
8	chr4:645800-656800	Weak transcription	Gastric	stomach
9	chr4:646800-650600	Enhancers	Brain Angular Gyrus	brain
10	chr4:647000-650000	Enhancers	Brain Anterior Caudate	brain
11	chr4:647200-651200	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr4:648200-649200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:648400-649000	Flanking Active TSS	Brain Hippocampus Middle	brain
14	chr4:648400-650200	Enhancers	Brain Substantia Nigra	brain
15	chr4:648400-657000	Weak transcription	Right Ventricle	heart
16	chr4:648600-648800	Flanking Active TSS	Brain Cingulate Gyrus	brain
17	chr4:648600-648800	Bivalent Enhancer	HepG2	liver
18	chr4:648600-649000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr4:648600-649000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr4:648600-649600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr4:648600-650000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
22	chr4:648600-650600	Enhancers	Spleen	Spleen

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