Variant report

Variant	rs6458814
Chromosome Location	chr6:13423292-13423293
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	chr6:13422912..13426230-chr6:13485786..13488463,3	MCF-7	breast:
2	chr6:13421809..13424895-chr6:13440143..13443244,3	MCF-7	breast:

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

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1345031	0.91[EUR][1000 genomes]
rs1345032	0.91[EUR][1000 genomes]
rs1550520	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1550521	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2119481	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2119482	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2119484	0.83[EUR][1000 genomes]
rs2165419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4145562	0.87[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs4454121	0.82[EUR][1000 genomes]
rs4715251	0.81[GIH][hapmap]
rs4715261	0.82[EUR][1000 genomes]
rs476138	0.83[EUR][1000 genomes]
rs478630	0.95[CEU][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs478804	0.95[CEU][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs480648	0.95[CEU][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs485804	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs490443	0.89[EUR][1000 genomes]
rs500197	0.95[CEU][hapmap]
rs500293	0.95[CEU][hapmap];0.83[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs503117	0.83[EUR][1000 genomes]
rs508153	0.83[EUR][1000 genomes]
rs519657	0.82[EUR][1000 genomes]
rs519890	0.95[CEU][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs536916	0.95[CEU][hapmap]
rs536998	0.95[CEU][hapmap];0.92[TSI][hapmap]
rs550403	0.88[EUR][1000 genomes]
rs558126	0.83[EUR][1000 genomes]
rs558242	0.83[EUR][1000 genomes]
rs559612	0.95[CEU][hapmap]
rs563424	0.81[EUR][1000 genomes]
rs564361	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs62385763	0.87[ASN][1000 genomes]
rs6458815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6910652	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs821299	0.81[EUR][1000 genomes]
rs9296672	0.87[CHB][hapmap];0.94[CHD][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.87[ASN][1000 genomes]
rs935061	0.87[ASN][1000 genomes]
rs9357727	0.84[EUR][1000 genomes]
rs9370104	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9395768	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9395770	0.82[EUR][1000 genomes]
rs9463764	0.86[CHB][hapmap];0.89[JPT][hapmap];0.87[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	nsv1033620	chr6:13419730-13571788	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6458814	C6orf114	cis	cerebellum	SCAN
rs6458814	GFOD1	cis	cerebellum	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13411600-13424200	Enhancers	Right Ventricle	heart
2	chr6:13417200-13424200	Enhancers	Brain Angular Gyrus	brain
3	chr6:13417600-13424000	Enhancers	Brain Cingulate Gyrus	brain
4	chr6:13417800-13424000	Enhancers	Adipose Nuclei	Adipose
5	chr6:13417800-13424200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
6	chr6:13417800-13424200	Enhancers	Left Ventricle	heart
7	chr6:13417800-13424600	Enhancers	Right Atrium	heart
8	chr6:13417800-13424800	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr6:13417800-13427000	Enhancers	Psoas Muscle	Psoas
10	chr6:13419200-13424200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr6:13419200-13428200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr6:13419400-13424000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
13	chr6:13419400-13429800	Enhancers	Fetal Lung	lung
14	chr6:13419600-13424200	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr6:13420000-13424000	Enhancers	Brain Substantia Nigra	brain
16	chr6:13420200-13427600	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr6:13420200-13430000	Enhancers	Fetal Stomach	stomach
18	chr6:13420400-13423800	Enhancers	Duodenum Smooth Muscle	Duodenum
19	chr6:13420400-13425400	Weak transcription	NHEK	skin
20	chr6:13420400-13427400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr6:13420600-13423600	Weak transcription	Esophagus	oesophagus
22	chr6:13420600-13425400	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr6:13420600-13425800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr6:13420600-13428000	Weak transcription	Thymus	Thymus
25	chr6:13420800-13425600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr6:13421000-13425400	Weak transcription	Liver	Liver
27	chr6:13421000-13425400	Weak transcription	Placenta	Placenta
28	chr6:13421000-13427200	Weak transcription	Primary B cells from cord blood	blood
29	chr6:13421200-13425200	Weak transcription	Primary B cells from peripheral blood	blood
30	chr6:13421200-13426400	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr6:13421400-13423400	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr6:13421400-13424200	Enhancers	H1 Cell Line	embryonic stem cell
33	chr6:13421400-13426600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr6:13421400-13427800	Weak transcription	Primary T cells from cord blood	blood
35	chr6:13421600-13423800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr6:13421600-13424000	Enhancers	Fetal Muscle Leg	muscle
37	chr6:13421800-13423400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr6:13421800-13423400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr6:13421800-13423600	Enhancers	Rectal Smooth Muscle	rectum
40	chr6:13421800-13423800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
41	chr6:13421800-13423800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr6:13421800-13423800	Enhancers	Brain Germinal Matrix	brain
43	chr6:13421800-13423800	Enhancers	Fetal Kidney	kidney
44	chr6:13421800-13424000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr6:13421800-13424000	Enhancers	Aorta	Aorta
46	chr6:13421800-13424000	Flanking Active TSS	Stomach Smooth Muscle	stomach
47	chr6:13421800-13424200	Enhancers	H9 Cell Line	embryonic stem cell
48	chr6:13422000-13424000	Enhancers	NHLF	lung
49	chr6:13422000-13424600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr6:13422000-13427800	Weak transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links