Variant report

Variant	rs565013
Chromosome Location	chr6:13399703-13399704
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13398336..13400389-chr6:13402109..13404070,2	K562	blood:
2	chr6:13397579..13400126-chr6:13573111..13574727,2	MCF-7	breast:
3	chr6:13397740..13400586-chr6:13613823..13615794,2	K562	blood:

Variant related genes	Relation type
ENSG00000261071	Chromatin interaction
ENSG00000225921	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10807437	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11753720	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11754291	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11758233	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1837701	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2119483	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2327673	0.83[EUR][1000 genomes]
rs4145562	1.00[CEU][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs4715251	0.80[CHD][hapmap]
rs478630	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs478804	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs480648	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs485804	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs487607	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs488885	0.80[ASN][1000 genomes]
rs494026	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs500197	0.91[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs500293	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs513613	0.89[ASN][1000 genomes]
rs519890	0.87[CHB][hapmap]
rs520828	0.83[ASN][1000 genomes]
rs523221	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs536916	0.91[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs536998	0.91[CHB][hapmap];0.92[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs559612	0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs563662	0.89[ASN][1000 genomes]
rs564361	0.88[CHB][hapmap];0.80[JPT][hapmap]
rs62385763	0.81[EUR][1000 genomes]
rs62386724	0.83[ASN][1000 genomes]
rs62386725	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62386727	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7742086	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs821298	0.89[ASN][1000 genomes]
rs821300	0.89[ASN][1000 genomes]
rs9296672	0.95[CEU][hapmap];0.82[GIH][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs935061	0.81[EUR][1000 genomes]
rs9357720	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9463764	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs9474117	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]

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
rs565013	GFOD1	cis	cerebellum	SCAN
rs565013	C6orf114	cis	cerebellum	SCAN

Chromatin state (count:55 , 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	chr6:13395600-13402800	Enhancers	Fetal Heart	heart
3	chr6:13396000-13404400	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr6:13396200-13407000	Weak transcription	Gastric	stomach
5	chr6:13396400-13404400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:13396600-13405800	Weak transcription	HepG2	liver
7	chr6:13396800-13404400	Weak transcription	NHLF	lung
8	chr6:13397000-13404600	Weak transcription	Aorta	Aorta
9	chr6:13397200-13399800	Enhancers	Brain Cingulate Gyrus	brain
10	chr6:13397200-13400000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:13398000-13404400	Weak transcription	Esophagus	oesophagus
12	chr6:13398000-13404600	Weak transcription	Small Intestine	intestine
13	chr6:13398000-13406000	Weak transcription	Lung	lung
14	chr6:13398200-13406800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr6:13398400-13400600	Enhancers	Stomach Smooth Muscle	stomach
16	chr6:13398400-13400600	Enhancers	GM12878-XiMat	blood
17	chr6:13398400-13400600	Weak transcription	K562	blood
18	chr6:13398400-13400800	Weak transcription	HUVEC	blood vessel
19	chr6:13398400-13407400	Weak transcription	Placenta	Placenta
20	chr6:13398600-13400200	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr6:13398600-13400400	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr6:13398600-13406000	Weak transcription	Primary B cells from cord blood	blood
23	chr6:13398800-13400200	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr6:13399000-13400400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr6:13399000-13400400	Weak transcription	Primary B cells from peripheral blood	blood
26	chr6:13399000-13400400	Weak transcription	Colon Smooth Muscle	Colon
27	chr6:13399000-13401000	Weak transcription	HMEC	breast
28	chr6:13399000-13404400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr6:13399000-13404400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr6:13399000-13404600	Weak transcription	Primary hematopoietic stem cells	blood
31	chr6:13399000-13404800	Weak transcription	Spleen	Spleen
32	chr6:13399200-13400000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr6:13399200-13401200	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr6:13399200-13401600	Enhancers	Right Atrium	heart
35	chr6:13399200-13403600	Weak transcription	Hela-S3	cervix
36	chr6:13399200-13404000	Weak transcription	Brain Angular Gyrus	brain
37	chr6:13399200-13404000	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr6:13399200-13404400	Weak transcription	Adipose Nuclei	Adipose
39	chr6:13399200-13404400	Weak transcription	Psoas Muscle	Psoas
40	chr6:13399200-13404400	Weak transcription	A549	lung
41	chr6:13399200-13404600	Weak transcription	HSMMtube	muscle
42	chr6:13399200-13406800	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr6:13399400-13400800	Weak transcription	Right Ventricle	heart
44	chr6:13399400-13401000	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr6:13399400-13401200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr6:13399400-13404400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr6:13399400-13404400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr6:13399400-13404400	Weak transcription	Brain Hippocampus Middle	brain
49	chr6:13399400-13404400	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr6:13399400-13404400	Weak transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links