Variant report

Variant	rs13185955
Chromosome Location	chr5:89822464-89822465
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:89821851-89826472	K562	blood:	n/a	n/a
2	POLR2A	chr5:89821783-89823769	GM12878	blood:	n/a	n/a
3	POLR2A	chr5:89822443-89822474	ProgFib	skin:	n/a	n/a
4	POLR2A	chr5:89822095-89826185	IMR90	lung:	n/a	n/a
5	BACH1	chr5:89822360-89822688	K562	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:89777835..89781277-chr5:89821033..89823702,3	K562	blood:
2	chr5:89822248..89824854-chr5:89913620..89915921,2	K562	blood:
3	chr5:89765101..89767054-chr5:89819920..89822582,2	K562	blood:
4	chr5:89821102..89822996-chr5:89857418..89859041,2	K562	blood:
5	chr5:89821999..89823611-chr5:89823888..89826662,2	MCF-7	breast:
6	chr5:89810981..89813583-chr5:89821226..89822873,2	MCF-7	breast:
7	chr5:89768691..89773005-chr5:89822332..89827140,9	MCF-7	breast:
8	chr5:89821919..89824561-chr5:89840686..89844146,3	MCF-7	breast:
9	chr5:89818873..89823263-chr5:89823614..89827101,4	MCF-7	breast:

No data

Variant related genes	Relation type
GPR98	TF binding region
ENSG00000176018	Chromatin interaction
ENSG00000176055	Chromatin interaction
ENSG00000113356	Chromatin interaction
ENSG00000164199	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 1 )

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	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1047787	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10514327	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.87[AMR][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];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[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];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13182165	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1533603	0.85[JPT][hapmap]
rs1673378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];0.86[EUR][1000 genomes]
rs1700511	0.92[JPT][hapmap]
rs1812737	0.97[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	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35407205	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3805483	1.00[CHB][hapmap];0.82[CHD][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs474800	0.84[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]
rs499148	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]
rs501640	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs502596	0.92[JPT][hapmap]
rs552314	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs558809	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs587818	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs603015	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[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]
rs603870	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs616379	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[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];0.84[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs623761	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs637442	0.92[JPT][hapmap]
rs6452906	0.85[JPT][hapmap]
rs645652	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs648430	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs666659	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs67376567	0.86[AMR][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];0.85[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];0.88[TSI][hapmap];0.84[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];0.89[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6898209	0.85[JPT][hapmap]
rs7703588	0.85[JPT][hapmap]
rs7716979	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7717423	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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:7 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13185955	LYSMD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89773800-89824400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:89780600-89822600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr5:89793800-89823400	Weak transcription	Hela-S3	cervix
4	chr5:89797600-89824200	Weak transcription	Brain Angular Gyrus	brain
5	chr5:89802600-89824600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:89805600-89823200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr5:89809000-89824000	Weak transcription	Right Ventricle	heart
8	chr5:89809000-89824400	Weak transcription	Psoas Muscle	Psoas
9	chr5:89809200-89824600	Weak transcription	Spleen	Spleen
10	chr5:89810400-89822800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr5:89810600-89824400	Weak transcription	Lung	lung
12	chr5:89810800-89824400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr5:89810800-89824400	Weak transcription	Esophagus	oesophagus
14	chr5:89811000-89824000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr5:89811000-89824400	Weak transcription	Pancreas	Pancrea
16	chr5:89813000-89823400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr5:89813400-89822800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:89813400-89824200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr5:89813400-89824400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr5:89813600-89823400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr5:89814200-89822600	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr5:89814800-89824000	Weak transcription	HSMMtube	muscle
23	chr5:89814800-89824200	Weak transcription	Brain Germinal Matrix	brain
24	chr5:89815000-89823800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr5:89815000-89824400	Weak transcription	Gastric	stomach
26	chr5:89815200-89823000	Weak transcription	A549	lung
27	chr5:89815200-89823800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr5:89815200-89824400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr5:89815200-89824400	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr5:89815200-89824400	Weak transcription	Brain Substantia Nigra	brain
31	chr5:89816200-89822800	Weak transcription	HMEC	breast
32	chr5:89816400-89824200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr5:89816600-89824000	Weak transcription	Aorta	Aorta
34	chr5:89816600-89824200	Weak transcription	Fetal Brain Male	brain
35	chr5:89816600-89824200	Weak transcription	Ovary	ovary
36	chr5:89817400-89824000	Weak transcription	Fetal Kidney	kidney
37	chr5:89817600-89824200	Weak transcription	Fetal Muscle Leg	muscle
38	chr5:89818000-89822600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr5:89818000-89824200	Weak transcription	Brain Hippocampus Middle	brain
40	chr5:89818200-89823200	Weak transcription	NHLF	lung
41	chr5:89818200-89824200	Weak transcription	Fetal Muscle Trunk	muscle
42	chr5:89818200-89824200	Weak transcription	Fetal Stomach	stomach
43	chr5:89818200-89824400	Weak transcription	Left Ventricle	heart
44	chr5:89818400-89822600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr5:89818600-89823400	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr5:89818600-89824000	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr5:89819000-89823400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr5:89819800-89822600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr5:89820000-89823600	Weak transcription	Primary hematopoietic stem cells	blood
50	chr5:89820000-89824000	Weak transcription	Colonic Mucosa	Colon

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