Variant report

Variant	rs2165419
Chromosome Location	chr6:13422242-13422243
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	chr6:13421809..13424895-chr6:13440143..13443244,3	MCF-7	breast:
2	chr6:13419746..13422416-chr6:13574078..13576571,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000124523	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1345031	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1345032	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1550520	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1550521	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2119481	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[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];0.88[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2119484	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4145562	0.87[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs4454121	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4715251	0.86[GIH][hapmap];0.84[MEX][hapmap]
rs4715261	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs476138	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs478630	0.95[CEU][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs478804	0.95[CEU][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs480648	0.95[CEU][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs485804	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs490443	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs500197	0.95[CEU][hapmap]
rs500293	0.95[CEU][hapmap];0.88[GIH][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs503117	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs508153	0.86[AMR][1000 genomes];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];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs536916	0.95[CEU][hapmap]
rs536998	0.95[CEU][hapmap];0.85[GIH][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap]
rs550403	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs558126	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs558242	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs559612	0.95[CEU][hapmap]
rs563424	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs564361	0.93[CEU][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs566320	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62385763	0.87[ASN][1000 genomes]
rs6458814	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]
rs6458815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6910652	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs821299	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9296672	0.87[CHB][hapmap];0.94[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs935061	0.87[ASN][1000 genomes]
rs9357727	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9370104	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9395768	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9395770	0.83[EUR][1000 genomes]
rs9463764	0.86[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs9474117	0.83[MEX][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	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
rs2165419	GFOD1	cis	cerebellum	SCAN
rs2165419	C6orf114	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13408600-13422600	Weak transcription	HSMM	muscle
2	chr6:13408800-13423000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr6:13411600-13424200	Enhancers	Right Ventricle	heart
4	chr6:13415400-13422600	Weak transcription	Gastric	stomach
5	chr6:13417200-13424200	Enhancers	Brain Angular Gyrus	brain
6	chr6:13417600-13424000	Enhancers	Brain Cingulate Gyrus	brain
7	chr6:13417800-13424000	Enhancers	Adipose Nuclei	Adipose
8	chr6:13417800-13424200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
9	chr6:13417800-13424200	Enhancers	Left Ventricle	heart
10	chr6:13417800-13424600	Enhancers	Right Atrium	heart
11	chr6:13417800-13424800	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr6:13417800-13427000	Enhancers	Psoas Muscle	Psoas
13	chr6:13418800-13422600	Weak transcription	HepG2	liver
14	chr6:13418800-13422600	Enhancers	HUVEC	blood vessel
15	chr6:13418800-13422800	Enhancers	Fetal Heart	heart
16	chr6:13419200-13424200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr6:13419200-13428200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr6:13419400-13424000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
19	chr6:13419400-13429800	Enhancers	Fetal Lung	lung
20	chr6:13419600-13422600	Enhancers	Lung	lung
21	chr6:13419600-13424200	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr6:13419800-13422800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:13419800-13422800	Enhancers	Fetal Muscle Trunk	muscle
24	chr6:13420000-13422400	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr6:13420000-13423000	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr6:13420000-13424000	Enhancers	Brain Substantia Nigra	brain
27	chr6:13420200-13422600	Enhancers	HSMMtube	muscle
28	chr6:13420200-13427600	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr6:13420200-13430000	Enhancers	Fetal Stomach	stomach
30	chr6:13420400-13422400	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr6:13420400-13422800	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr6:13420400-13423000	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr6:13420400-13423200	Enhancers	Colon Smooth Muscle	Colon
34	chr6:13420400-13423200	Weak transcription	Pancreas	Pancrea
35	chr6:13420400-13423800	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr6:13420400-13425400	Weak transcription	NHEK	skin
37	chr6:13420400-13427400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr6:13420600-13423600	Weak transcription	Esophagus	oesophagus
39	chr6:13420600-13425400	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr6:13420600-13425800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr6:13420600-13428000	Weak transcription	Thymus	Thymus
42	chr6:13420800-13422400	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr6:13420800-13422600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr6:13420800-13422600	Weak transcription	Spleen	Spleen
45	chr6:13420800-13425600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr6:13421000-13422400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr6:13421000-13425400	Weak transcription	Liver	Liver
48	chr6:13421000-13425400	Weak transcription	Placenta	Placenta
49	chr6:13421000-13427200	Weak transcription	Primary B cells from cord blood	blood
50	chr6:13421200-13422400	Enhancers	HUES48 Cell Line	embryonic stem cell

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