Variant report

Variant	rs813218
Chromosome Location	chr3:99592596-99592597
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:99591437..99593701-chr3:99599542..99601612,3	K562	blood:
2	chr3:99582314..99585905-chr3:99590964..99594499,4	MCF-7	breast:
3	chr3:99589147..99593753-chr3:99593896..99597054,6	MCF-7	breast:
4	chr3:99591850..99594536-chr3:99980465..99982700,2	K562	blood:
5	chr3:99592456..99594885-chr3:99685238..99688172,2	MCF-7	breast:
6	chr3:99557106..99559830-chr3:99591722..99593222,2	K562	blood:

Variant related genes	Relation type
ENSG00000168386	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10936003	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11719468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1287284	0.84[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs13059754	0.84[CEU][hapmap];0.80[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.81[MKK][hapmap]
rs1384062	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs1610509	0.86[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap]
rs16841874	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1711564	0.82[LWK][hapmap];0.85[YRI][hapmap]
rs1718235	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4577503	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.83[MKK][hapmap];0.85[ASN][1000 genomes]
rs4928150	0.84[CEU][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs4928151	0.84[CEU][hapmap];0.94[JPT][hapmap]
rs4928230	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4928237	0.84[CEU][hapmap];0.94[JPT][hapmap]
rs58704213	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6440967	0.84[CEU][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs669676	0.83[ASW][hapmap];0.82[LWK][hapmap];0.85[YRI][hapmap]
rs6788750	0.84[LWK][hapmap];0.94[MKK][hapmap]
rs6802817	0.84[CEU][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs6806323	0.84[CEU][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs704571	0.94[JPT][hapmap]
rs704572	1.00[JPT][hapmap];0.90[YRI][hapmap]
rs704574	0.86[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap]
rs7613864	0.85[ASN][1000 genomes]
rs7649349	0.84[CEU][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs7650727	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs766778	0.84[CEU][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs792831	0.94[JPT][hapmap]
rs792833	0.86[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap]
rs792835	0.86[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap]
rs792836	0.94[JPT][hapmap]
rs792837	0.94[JPT][hapmap]
rs793437	0.83[ASN][1000 genomes]
rs793439	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs793443	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs793446	0.84[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs793450	0.95[LWK][hapmap];0.88[MKK][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes]
rs793456	0.82[ASN][1000 genomes]
rs793464	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.83[MKK][hapmap];0.85[ASN][1000 genomes]
rs793469	0.95[LWK][hapmap];0.90[MKK][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes]
rs793475	0.83[CEU][hapmap];0.83[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs793476	0.87[ASN][1000 genomes]
rs793482	0.86[LWK][hapmap];0.92[YRI][hapmap]
rs793483	0.82[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap]
rs793485	0.94[JPT][hapmap]
rs793497	0.90[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap]
rs793502	1.00[ASW][hapmap];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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs796976	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs902159	0.84[CEU][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap]
rs923472	0.84[CEU][hapmap];0.94[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	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Orofacial clefts	22863734	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs813218	OR5H6	cis	cerebellum	SCAN
rs813218	C3orf26	Cis_1M	lymphoblastoid	RTeQTL
rs813218	SENP7	cis	parietal	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99537200-99594400	Weak transcription	Esophagus	oesophagus
2	chr3:99563200-99593600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:99573200-99594000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr3:99575000-99593600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr3:99581400-99594000	Weak transcription	Primary B cells from peripheral blood	blood
6	chr3:99583600-99593600	Weak transcription	Primary B cells from cord blood	blood
7	chr3:99586200-99594000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr3:99587400-99592800	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr3:99587400-99594600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:99589400-99593000	Enhancers	Placenta Amnion	Placenta Amnion
11	chr3:99590000-99595800	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr3:99590200-99592600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:99590200-99595800	Active TSS	Right Atrium	heart
14	chr3:99590200-99596000	Active TSS	Skeletal Muscle Male	skeletal muscle
15	chr3:99590400-99592600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:99590400-99592800	Flanking Active TSS	Adipose Nuclei	Adipose
17	chr3:99590600-99593600	Enhancers	Stomach Mucosa	stomach
18	chr3:99590600-99595800	Active TSS	Ovary	ovary
19	chr3:99590600-99596400	Active TSS	Rectal Mucosa Donor 29	rectum
20	chr3:99590800-99594200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr3:99591000-99592600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:99591000-99592600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr3:99591000-99593000	Enhancers	HMEC	breast
24	chr3:99591000-99594000	Weak transcription	Liver	Liver
25	chr3:99591000-99594200	Weak transcription	Fetal Muscle Trunk	muscle
26	chr3:99591200-99592600	Flanking Active TSS	NH-A	brain
27	chr3:99591200-99593400	Active TSS	Left Ventricle	heart
28	chr3:99591200-99594400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:99591200-99594400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr3:99591200-99594400	Weak transcription	Lung	lung
31	chr3:99591200-99594400	Weak transcription	Pancreas	Pancrea
32	chr3:99591200-99595600	Active TSS	Right Ventricle	heart
33	chr3:99591400-99593200	Flanking Active TSS	HUVEC	blood vessel
34	chr3:99591400-99596200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:99591600-99592600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
36	chr3:99591600-99592600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr3:99591600-99592800	Transcr. at gene 5' and 3'	HSMM	muscle
38	chr3:99591600-99593000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr3:99591600-99593000	Flanking Active TSS	Fetal Intestine Large	intestine
40	chr3:99591600-99593400	Flanking Active TSS	Osteobl	bone
41	chr3:99591600-99594200	Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr3:99591600-99595600	Active TSS	Colonic Mucosa	Colon
43	chr3:99591600-99595600	Active TSS	Psoas Muscle	Psoas
44	chr3:99591600-99595600	Active TSS	HSMMtube	muscle
45	chr3:99591600-99596000	Active TSS	Stomach Smooth Muscle	stomach
46	chr3:99591600-99596000	Active TSS	NHLF	lung
47	chr3:99591600-99596400	Active TSS	Fetal Muscle Leg	muscle
48	chr3:99591600-99596800	Active TSS	Aorta	Aorta
49	chr3:99591800-99593400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:99591800-99594000	Flanking Active TSS	NHEK	skin

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