Variant report

Variant	rs6826407
Chromosome Location	chr4:89975033-89975034
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:89962640..89965457-chr4:89973321..89975706,2	K562	blood:
2	chr4:89963957..89965462-chr4:89973010..89975706,2	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10000140	0.87[CEU][hapmap];0.85[AMR][1000 genomes]
rs10024807	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10027874	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs10029662	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10030342	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs11097209	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11097210	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];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11097211	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];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12507819	0.82[AMR][1000 genomes]
rs13113298	0.86[CEU][hapmap]
rs13115669	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs13140085	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13150503	0.87[CEU][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs1343921	0.87[LWK][hapmap]
rs1588730	0.87[CEU][hapmap]
rs17014898	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17014901	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17014988	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2056012	0.90[AMR][1000 genomes]
rs28379646	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34378169	0.91[ASN][1000 genomes]
rs34693890	0.95[ASN][1000 genomes]
rs36048928	0.95[ASN][1000 genomes]
rs59385067	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61286299	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6532102	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67317338	0.95[ASN][1000 genomes]
rs6823660	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs6827398	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6853075	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6857969	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7660377	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7668782	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs7674344	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs874147	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9992522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9996559	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009354	chr4:89725914-89985155	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1007025	chr4:89837734-90098046	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv537176	chr4:89837734-90098046	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv461577	chr4:89904124-89986326	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv594807	chr4:89904124-89986326	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1002448	chr4:89933385-90128133	Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6826407	FAM13A	cis	cerebellum	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:89937200-89975600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:89944200-89978000	Weak transcription	Pancreas	Pancrea
3	chr4:89959000-89975400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr4:89963200-89975800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr4:89970600-89975200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr4:89972600-89975400	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr4:89972600-89975400	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr4:89973000-89975800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr4:89973200-89975600	Weak transcription	Fetal Muscle Leg	muscle
10	chr4:89973200-89977000	Weak transcription	Psoas Muscle	Psoas
11	chr4:89973400-89975200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr4:89973400-89976400	Weak transcription	Fetal Intestine Small	intestine
13	chr4:89973400-89976800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr4:89973400-89977800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr4:89973400-89977800	Weak transcription	Right Ventricle	heart
16	chr4:89973600-89975600	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr4:89973600-89977800	Weak transcription	Placenta	Placenta
18	chr4:89974000-89975200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr4:89974000-89975200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr4:89974000-89975400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr4:89974000-89976000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr4:89974200-89975400	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr4:89974200-89975600	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr4:89974400-89975200	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr4:89974400-89975200	Weak transcription	Fetal Heart	heart
26	chr4:89974400-89975200	Weak transcription	A549	lung
27	chr4:89974400-89975600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr4:89974400-89975600	Enhancers	Aorta	Aorta
29	chr4:89974400-89976000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr4:89974400-89976200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr4:89974600-89975400	Weak transcription	HMEC	breast
32	chr4:89974600-89975400	Weak transcription	HUVEC	blood vessel
33	chr4:89974600-89975600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr4:89974600-89975800	Weak transcription	Right Atrium	heart
35	chr4:89974600-89976400	Enhancers	Fetal Lung	lung
36	chr4:89974600-89976600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr4:89974800-89975200	Weak transcription	Ovary	ovary
38	chr4:89974800-89975400	Enhancers	K562	blood
39	chr4:89974800-89975800	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr4:89974800-89975800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr4:89974800-89975800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr4:89974800-89975800	Weak transcription	Fetal Kidney	kidney
43	chr4:89975000-89975200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr4:89975000-89975400	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr4:89975000-89975800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr4:89975000-89976000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr4:89975000-89976000	Active TSS	GM12878-XiMat	blood
48	chr4:89975000-89976200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr4:89975000-89976200	Weak transcription	NHDF-Ad	bronchial

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