Variant report

Variant	rs536998
Chromosome Location	chr6:13395585-13395586
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13394396..13395912-chr6:13486331..13488478,2	MCF-7	breast:
2	chr6:13383495..13385578-chr6:13393149..13396280,3	K562	blood:
3	chr6:13345896..13348764-chr6:13394110..13395798,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000187461	Chromatin interaction
ENSG00000237786	Chromatin interaction
ENSG00000145990	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10807437	0.86[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap]
rs11753720	0.89[ASN][1000 genomes]
rs1345031	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1345032	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1837701	0.89[ASN][1000 genomes]
rs2119481	0.95[CEU][hapmap]
rs2119482	0.91[CEU][hapmap];0.82[TSI][hapmap]
rs2119483	0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs2119484	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2165419	0.95[CEU][hapmap];0.85[GIH][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap]
rs4454121	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4715251	0.83[CEU][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.85[ASN][1000 genomes]
rs4715261	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs476138	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs478630	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs478804	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs480648	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs485804	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs487607	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs488885	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs490443	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs500197	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs500293	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs503117	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs508153	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs513613	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs519657	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs519890	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.87[JPT][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs520828	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs523221	0.89[ASN][1000 genomes]
rs536916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs544639	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs546507	0.83[ASN][1000 genomes]
rs550403	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs558126	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs558242	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs559565	0.83[CEU][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs559612	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs563424	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs563662	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs564361	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs565013	0.91[CHB][hapmap];0.92[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs566320	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62386724	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62386725	0.89[ASN][1000 genomes]
rs62386727	0.87[ASN][1000 genomes]
rs6458814	0.95[CEU][hapmap];0.92[TSI][hapmap]
rs6458815	0.95[CEU][hapmap];0.80[GIH][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap]
rs6910652	0.95[CEU][hapmap]
rs7742086	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs821298	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs821299	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs821300	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9357720	0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs9474117	0.86[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1034016	chr6:13248122-13418225	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs536998	GFOD1	cis	cerebellum	SCAN
rs536998	C6orf114	cis	cerebellum	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13368000-13404600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr6:13377800-13395600	Weak transcription	Aorta	Aorta
3	chr6:13382400-13397600	Weak transcription	Esophagus	oesophagus
4	chr6:13387000-13396000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:13393000-13395600	Weak transcription	Right Ventricle	heart
6	chr6:13393200-13395600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr6:13393200-13395600	Weak transcription	Fetal Heart	heart
8	chr6:13394600-13399000	Enhancers	Primary B cells from peripheral blood	blood
9	chr6:13395000-13396600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr6:13395000-13399000	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr6:13395200-13395600	Enhancers	GM12878-XiMat	blood
12	chr6:13395200-13395800	Enhancers	HUVEC	blood vessel
13	chr6:13395200-13396200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr6:13395200-13396200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr6:13395200-13396600	Enhancers	HepG2	liver
16	chr6:13395200-13398000	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr6:13395200-13398600	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr6:13395200-13398800	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr6:13395200-13398800	Enhancers	Stomach Mucosa	stomach
20	chr6:13395200-13399000	Enhancers	Primary hematopoietic stem cells	blood
21	chr6:13395200-13399200	Enhancers	Adipose Nuclei	Adipose
22	chr6:13395400-13395600	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr6:13395400-13395600	Flanking Active TSS	NHEK	skin
24	chr6:13395400-13395800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr6:13395400-13395800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr6:13395400-13395800	Enhancers	Brain Hippocampus Middle	brain
27	chr6:13395400-13395800	Enhancers	Stomach Smooth Muscle	stomach
28	chr6:13395400-13395800	Enhancers	HMEC	breast
29	chr6:13395400-13395800	Enhancers	HSMM	muscle
30	chr6:13395400-13396000	Enhancers	Muscle Satellite Cultured Cells	--
31	chr6:13395400-13396200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr6:13395400-13396200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr6:13395400-13396200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr6:13395400-13396200	Enhancers	Brain Cingulate Gyrus	brain
35	chr6:13395400-13396200	Enhancers	Fetal Intestine Small	intestine
36	chr6:13395400-13396200	Enhancers	Fetal Muscle Trunk	muscle
37	chr6:13395400-13396200	Enhancers	Gastric	stomach
38	chr6:13395400-13396200	Flanking Active TSS	Hela-S3	cervix
39	chr6:13395400-13396200	Flanking Active TSS	K562	blood
40	chr6:13395400-13396200	Enhancers	NH-A	brain
41	chr6:13395400-13396200	Enhancers	Osteobl	bone
42	chr6:13395400-13396400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr6:13395400-13396400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr6:13395400-13396600	Enhancers	NHDF-Ad	bronchial
45	chr6:13395400-13396800	Enhancers	Brain Substantia Nigra	brain
46	chr6:13395400-13396800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
47	chr6:13395400-13396800	Enhancers	NHLF	lung
48	chr6:13395400-13397000	Enhancers	Liver	Liver
49	chr6:13395400-13397000	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr6:13395400-13397000	Enhancers	Fetal Lung	lung

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