Variant report

Variant	rs4838620
Chromosome Location	chr10:49760827-49760828
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:49755429..49757315-chr10:49758822..49761538,2	K562	blood:
2	chr10:49760107..49762474-chr10:49763848..49765679,2	K562	blood:
3	chr10:49759621..49761193-chr10:49762687..49765041,2	MCF-7	breast:
4	chr10:49759388..49761002-chr10:49863863..49865018,17	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128805	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1078261	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11101383	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11598598	1.00[CHB][hapmap];0.95[MEX][hapmap];0.85[AMR][1000 genomes]
rs11599380	1.00[CHD][hapmap]
rs12766573	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1373793	1.00[CHD][hapmap]
rs1373795	1.00[CHB][hapmap]
rs1445150	0.81[CEU][hapmap]
rs1838571	0.81[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap]
rs1838572	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1867588	1.00[CHD][hapmap]
rs2004665	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4838419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4838619	0.87[EUR][1000 genomes]
rs6537567	0.81[CEU][hapmap];0.84[GIH][hapmap];0.85[TSI][hapmap]
rs7077561	0.85[EUR][1000 genomes]
rs7092639	0.86[CEU][hapmap]
rs7093632	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs747532	0.96[CEU][hapmap];0.97[GIH][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes]
rs7895981	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7911418	0.85[CEU][hapmap];0.94[GIH][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs7919520	1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs935265	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935266	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935267	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs935268	0.81[CEU][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs935269	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs935270	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs935276	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv895372	chr10:49576878-49933488	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4838620	SYT15	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49734400-49762400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr10:49739400-49762400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr10:49742600-49774800	Weak transcription	Aorta	Aorta
4	chr10:49751200-49771600	Weak transcription	Pancreas	Pancrea
5	chr10:49753400-49764400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr10:49755000-49761800	Weak transcription	Colon Smooth Muscle	Colon
7	chr10:49757400-49761600	Enhancers	HUVEC	blood vessel
8	chr10:49757400-49782200	Weak transcription	HSMMtube	muscle
9	chr10:49758200-49762400	Weak transcription	Right Atrium	heart
10	chr10:49758400-49762200	Weak transcription	HMEC	breast
11	chr10:49758600-49762000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr10:49759000-49761400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr10:49759200-49761000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr10:49759200-49761200	Enhancers	Primary B cells from peripheral blood	blood
15	chr10:49759200-49770400	Weak transcription	NH-A	brain
16	chr10:49759400-49763800	Enhancers	Brain Substantia Nigra	brain
17	chr10:49759600-49761400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr10:49759800-49761000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr10:49759800-49761000	Enhancers	Primary B cells from cord blood	blood
20	chr10:49759800-49761800	Enhancers	Brain Hippocampus Middle	brain
21	chr10:49759800-49763600	Enhancers	Brain Cingulate Gyrus	brain
22	chr10:49759800-49764200	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr10:49760000-49761200	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr10:49760200-49761000	Genic enhancers	Osteobl	bone
25	chr10:49760200-49761800	Weak transcription	NHDF-Ad	bronchial
26	chr10:49760200-49764600	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr10:49760400-49761000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr10:49760400-49761200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr10:49760400-49761200	Enhancers	Lung	lung
30	chr10:49760400-49762200	Weak transcription	Fetal Muscle Leg	muscle
31	chr10:49760600-49761400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr10:49760600-49762000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr10:49760600-49762200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr10:49760600-49762400	Weak transcription	Right Ventricle	heart
35	chr10:49760800-49762000	Weak transcription	Brain Angular Gyrus	brain
36	chr10:49760800-49762200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr10:49760800-49762200	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr10:49760800-49762400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr10:49760800-49765000	Strong transcription	NHLF	lung
40	chr10:49760800-49765400	Strong transcription	HSMM	muscle
41	chr10:49760800-49765600	Strong transcription	Muscle Satellite Cultured Cells	--
42	chr10:49760800-49768800	Weak transcription	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links