Variant report

Variant	rs499148
Chromosome Location	chr5:89826726-89826727
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr5:89823293-89826982	K562	blood:	n/a	chr5:89826147-89826157 chr5:89826147-89826157 chr5:89826149-89826156 chr5:89826148-89826156 chr5:89826148-89826156 chr5:89826147-89826157

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:89703358..89707086-chr5:89823955..89827154,6	MCF-7	breast:
2	chr5:89826684..89828882-chr5:89853247..89854802,2	K562	blood:
3	chr5:89825930..89827528-chr5:89867274..89868949,2	MCF-7	breast:
4	chr5:89825899..89828736-chr5:89905925..89909224,3	K562	blood:
5	chr5:89825541..89827508-chr5:89852797..89855537,2	MCF-7	breast:
6	chr5:89708413..89711602-chr5:89825612..89828655,3	K562	blood:
7	chr5:89825681..89827224-chr5:89844315..89846523,2	K562	blood:
8	chr5:89766469..89774126-chr5:89823341..89829105,11	K562	blood:
9	chr5:89822684..89827061-chr5:89851623..89857043,7	MCF-7	breast:
10	chr5:89705290..89707109-chr5:89824364..89826854,3	MCF-7	breast:
11	chr5:89826199..89831045-chr5:89834037..89838315,7	K562	blood:
12	chr5:89825598..89829055-chr5:89851441..89854747,4	K562	blood:
13	chr5:89704960..89708059-chr5:89823269..89827144,6	K562	blood:
14	chr5:89768855..89773751-chr5:89822671..89829297,12	K562	blood:
15	chr5:89768691..89773005-chr5:89822332..89827140,9	MCF-7	breast:
16	chr5:89703407..89707223-chr5:89822965..89826833,10	K562	blood:
17	chr5:89767818..89772796-chr5:89823286..89827702,11	MCF-7	breast:
18	chr5:89734834..89736191-chr5:89825533..89826967,10	K562	blood:

No data

Variant related genes	Relation type
LYSMD3	TF binding region
ENSG00000255647	Chromatin interaction
ENSG00000153140	Chromatin interaction
ENSG00000164199	Chromatin interaction
ENSG00000113356	Chromatin interaction
ENSG00000176055	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10036980	0.85[JPT][hapmap]
rs10043836	0.85[JPT][hapmap]
rs10058765	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs10060427	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs10062714	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs10062924	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs10067181	0.85[JPT][hapmap]
rs10068473	0.85[JPT][hapmap]
rs10072105	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs1028191	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs1028192	0.85[JPT][hapmap]
rs1033290	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs10462342	0.82[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap]
rs10473936	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1047787	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10514327	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10514333	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs10942596	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs10942597	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10942605	0.85[JPT][hapmap]
rs10942606	0.85[JPT][hapmap]
rs1160121	0.85[JPT][hapmap]
rs11743030	0.81[CHB][hapmap]
rs12188928	0.85[JPT][hapmap]
rs12516985	0.83[JPT][hapmap]
rs12655180	0.80[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13182165	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13185955	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1533603	0.85[JPT][hapmap]
rs1673378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1673379	0.92[JPT][hapmap]
rs16868957	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs1700510	0.96[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap];0.82[YRI][hapmap];0.88[EUR][1000 genomes]
rs1700511	0.92[JPT][hapmap]
rs1812737	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1878878	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs1993474	0.84[JPT][hapmap]
rs2176624	0.85[JPT][hapmap]
rs2222242	0.85[JPT][hapmap]
rs2366771	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs2366773	0.92[JPT][hapmap]
rs2366774	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs2366777	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs3087840	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35407205	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3805483	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];0.88[ASN][1000 genomes]
rs474800	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs490812	0.92[JPT][hapmap]
rs4916681	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs4916684	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs4916686	0.85[JPT][hapmap]
rs4916813	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs4916815	0.83[JPT][hapmap]
rs498491	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs501640	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs502596	0.92[JPT][hapmap]
rs552314	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs558809	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs587818	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs603015	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs603870	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs616379	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs617379	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs618355	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs623761	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs637442	0.92[JPT][hapmap]
rs6452906	0.85[JPT][hapmap]
rs645652	0.81[CHB][hapmap];0.82[CHD][hapmap];0.92[JPT][hapmap]
rs648430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs666659	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs67376567	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6863710	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs6878917	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs6881412	0.85[JPT][hapmap]
rs6883872	0.92[JPT][hapmap]
rs6888355	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs688956	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs688960	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs6897910	1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6898209	0.85[JPT][hapmap]
rs7703588	0.85[JPT][hapmap]
rs7716979	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7717423	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7721198	0.82[JPT][hapmap]
rs7723259	0.84[JPT][hapmap]
rs7724806	0.85[JPT][hapmap]
rs7726624	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs7729703	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs7732169	0.85[JPT][hapmap]
rs9293550	0.85[JPT][hapmap]
rs963866	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs977906	0.85[JPT][hapmap]
rs9790907	0.81[CHB][hapmap];0.92[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021142	chr5:89102893-89897826	Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv537804	chr5:89102893-89897826	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	55 gene(s)	inside rSNPs	diseases
3	nsv917025	chr5:89208994-89855436	Enhancers Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv432750	chr5:89410113-90137144	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv432751	chr5:89457044-90090444	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
7	nsv882365	chr5:89770768-89882618	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv882366	chr5:89826726-89894564	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs499148	GPR98	cis	cerebellum	SCAN
rs499148	LYSMD3	cis	normal skin	skin_eQTL
rs499148	LYSMD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89824400-89826800	Active TSS	Thymus	Thymus
2	chr5:89826000-89826800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:89826000-89826800	Enhancers	Small Intestine	intestine
4	chr5:89826200-89826800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr5:89826200-89826800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr5:89826200-89826800	Flanking Active TSS	Adipose Nuclei	Adipose
7	chr5:89826200-89826800	Flanking Active TSS	Brain Angular Gyrus	brain
8	chr5:89826200-89826800	Flanking Active TSS	Brain Anterior Caudate	brain
9	chr5:89826200-89826800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
10	chr5:89826200-89826800	Flanking Active TSS	Colon Smooth Muscle	Colon
11	chr5:89826200-89826800	Flanking Active TSS	Rectal Smooth Muscle	rectum
12	chr5:89826200-89826800	Flanking Active TSS	Stomach Smooth Muscle	stomach
13	chr5:89826200-89827000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr5:89826200-89827000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr5:89826200-89827000	Flanking Active TSS	Liver	Liver
16	chr5:89826200-89827000	Flanking Active TSS	Brain Cingulate Gyrus	brain
17	chr5:89826200-89827200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr5:89826200-89827200	Flanking Active TSS	K562	blood
19	chr5:89826200-89827400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr5:89826200-89842800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr5:89826400-89826800	Enhancers	H1 Cell Line	embryonic stem cell
22	chr5:89826400-89826800	Enhancers	Primary B cells from cord blood	blood
23	chr5:89826400-89826800	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr5:89826400-89826800	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr5:89826400-89826800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr5:89826400-89826800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr5:89826400-89826800	Flanking Active TSS	Brain Hippocampus Middle	brain
28	chr5:89826400-89826800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr5:89826400-89826800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr5:89826400-89826800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr5:89826400-89826800	Flanking Active TSS	Fetal Brain Female	brain
32	chr5:89826400-89826800	Enhancers	A549	lung
33	chr5:89826400-89826800	Enhancers	GM12878-XiMat	blood
34	chr5:89826400-89827000	Flanking Active TSS	Brain Germinal Matrix	brain
35	chr5:89826400-89827200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
36	chr5:89826400-89827400	Enhancers	Brain Substantia Nigra	brain
37	chr5:89826600-89826800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr5:89826600-89826800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr5:89826600-89826800	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr5:89826600-89826800	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr5:89826600-89826800	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr5:89826600-89826800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr5:89826600-89826800	Enhancers	Aorta	Aorta
44	chr5:89826600-89826800	Enhancers	Fetal Intestine Large	intestine
45	chr5:89826600-89826800	Enhancers	Rectal Mucosa Donor 29	rectum
46	chr5:89826600-89826800	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr5:89826600-89826800	Enhancers	Dnd41	blood
48	chr5:89826600-89826800	Enhancers	HMEC	breast
49	chr5:89826600-89826800	Active TSS	Monocytes-CD14+_RO01746	blood
50	chr5:89826600-89826800	Enhancers	NHLF	lung

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