Variant report

Variant	rs467300
Chromosome Location	chr5:58509816-58509817
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10074426	1.00[JPT][hapmap]
rs13155290	1.00[JPT][hapmap]
rs149084	0.84[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs149108	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs153966	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs153967	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs153980	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs153983	0.82[ASN][1000 genomes]
rs1867724	0.81[TSI][hapmap]
rs255579	0.84[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs425384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72765909	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72765911	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	esv3350487	chr5:58509777-58510148	Genic enhancers Strong transcription Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs467300	ACTBL2	cis	parietal	SCAN
rs467300	SKIV2L2	cis	parietal	SCAN
rs467300	FLJ37543	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58474400-58520000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr5:58485000-58518800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr5:58485600-58512400	Weak transcription	Pancreas	Pancrea
4	chr5:58485600-58518200	Weak transcription	Fetal Muscle Trunk	muscle
5	chr5:58490000-58511600	Weak transcription	Gastric	stomach
6	chr5:58490400-58519200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr5:58491400-58515600	Weak transcription	Fetal Stomach	stomach
8	chr5:58492400-58510600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr5:58494400-58513600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr5:58494600-58510000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr5:58496200-58515600	Weak transcription	Fetal Kidney	kidney
12	chr5:58501800-58512400	Weak transcription	Fetal Brain Male	brain
13	chr5:58502000-58517200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr5:58503200-58514400	Weak transcription	HUVEC	blood vessel
15	chr5:58504200-58510200	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr5:58504600-58510200	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr5:58505800-58512000	Genic enhancers	A549	lung
18	chr5:58506200-58512600	Enhancers	Pancreatic Islets	Pancreatic Islet
19	chr5:58506400-58512400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr5:58506400-58518200	Weak transcription	Left Ventricle	heart
21	chr5:58506400-58520400	Weak transcription	Stomach Mucosa	stomach
22	chr5:58506600-58513200	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr5:58509000-58510000	Enhancers	Psoas Muscle	Psoas
24	chr5:58509000-58510000	Enhancers	Hela-S3	cervix
25	chr5:58509200-58510200	Weak transcription	Fetal Intestine Large	intestine
26	chr5:58509200-58510600	Genic enhancers	Colon Smooth Muscle	Colon
27	chr5:58509200-58518400	Weak transcription	Brain Hippocampus Middle	brain
28	chr5:58509400-58510200	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr5:58509400-58518800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr5:58509600-58510000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
31	chr5:58509600-58510600	Genic enhancers	Rectal Mucosa Donor 31	rectum
32	chr5:58509600-58511000	Enhancers	Fetal Lung	lung
33	chr5:58509800-58510200	Genic enhancers	Fetal Heart	heart
34	chr5:58509800-58510200	Strong transcription	Fetal Muscle Leg	muscle
35	chr5:58509800-58511000	Strong transcription	Stomach Smooth Muscle	stomach
36	chr5:58509800-58512000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr5:58509800-58512400	Weak transcription	Fetal Intestine Small	intestine

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