Variant report

Variant	rs27727
Chromosome Location	chr5:58500382-58500383
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10051456	0.83[AMR][1000 genomes]
rs10067048	0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs10074426	0.92[CEU][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes]
rs13155290	0.92[CEU][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs154222	0.85[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.88[ASN][1000 genomes]
rs154224	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27172	0.85[CEU][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs27641	0.86[ASN][1000 genomes]
rs7724814	0.92[CEU][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9292197	0.92[CEU][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9292198	1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830363	chr5:57893949-58555491	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1023570	chr5:58486384-58537849	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv598252	chr5:58487764-58618889	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs27727	ACTBL2	cis	parietal	SCAN
rs27727	TPH1	trans	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58474400-58520000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr5:58484800-58501200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr5:58485000-58505200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:58485000-58518800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr5:58485600-58500400	Weak transcription	Psoas Muscle	Psoas
6	chr5:58485600-58501600	Weak transcription	HUVEC	blood vessel
7	chr5:58485600-58512400	Weak transcription	Pancreas	Pancrea
8	chr5:58485600-58518200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr5:58486000-58508600	Weak transcription	Fetal Intestine Large	intestine
10	chr5:58489800-58500400	Weak transcription	Right Ventricle	heart
11	chr5:58490000-58500400	Weak transcription	Left Ventricle	heart
12	chr5:58490000-58509800	Weak transcription	Fetal Muscle Leg	muscle
13	chr5:58490000-58511600	Weak transcription	Gastric	stomach
14	chr5:58490400-58501200	Weak transcription	Fetal Heart	heart
15	chr5:58490400-58519200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr5:58491400-58505800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr5:58491400-58509000	Weak transcription	Fetal Intestine Small	intestine
18	chr5:58491400-58515600	Weak transcription	Fetal Stomach	stomach
19	chr5:58492000-58505600	Weak transcription	Hela-S3	cervix
20	chr5:58492400-58510600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr5:58493400-58500800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr5:58494400-58500400	Weak transcription	Brain Substantia Nigra	brain
23	chr5:58494400-58513600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr5:58494600-58510000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr5:58496000-58500800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr5:58496000-58501600	Weak transcription	Fetal Lung	lung
27	chr5:58496200-58515600	Weak transcription	Fetal Kidney	kidney
28	chr5:58498600-58506200	Weak transcription	Aorta	Aorta
29	chr5:58498800-58500400	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr5:58498800-58501800	Genic enhancers	A549	lung
31	chr5:58500200-58503200	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr5:58500200-58503600	Enhancers	Colon Smooth Muscle	Colon
33	chr5:58500200-58506400	Enhancers	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links