Variant report

Variant	rs6792417
Chromosome Location	chr3:119391206-119391207
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119388635..119391771-chr3:119394131..119397043,3	MCF-7	breast:
2	chr3:119328437..119330333-chr3:119390205..119392685,2	K562	blood:
3	chr3:119384220..119388638-chr3:119390311..119393902,4	K562	blood:
4	chr3:119389108..119393521-chr3:119393632..119397776,6	MCF-7	breast:
5	chr3:119389471..119391263-chr3:119394151..119396440,3	K562	blood:

Variant related genes	Relation type
ENSG00000138495	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1124723	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1124724	0.90[AMR][1000 genomes]
rs11914676	0.93[ASN][1000 genomes]
rs11923223	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11925762	0.82[AFR][1000 genomes]
rs12487499	0.87[ASN][1000 genomes]
rs12488460	0.87[ASN][1000 genomes]
rs12490779	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12492456	0.90[ASN][1000 genomes]
rs12493022	0.89[AMR][1000 genomes]
rs13061374	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13061497	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1403631	0.87[ASN][1000 genomes]
rs1525836	0.87[ASN][1000 genomes]
rs16830115	0.90[ASN][1000 genomes]
rs16830291	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17203235	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1797827	0.90[ASN][1000 genomes]
rs1851611	0.90[AMR][1000 genomes]
rs1872432	0.89[ASN][1000 genomes]
rs1905788	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1905790	0.86[AMR][1000 genomes]
rs1985121	0.87[ASN][1000 genomes]
rs2102627	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2137619	0.90[AMR][1000 genomes]
rs2280578	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2670292	0.87[ASN][1000 genomes]
rs2688629	0.90[ASN][1000 genomes]
rs2688630	0.90[ASN][1000 genomes]
rs2688631	0.90[ASN][1000 genomes]
rs2688634	0.84[ASN][1000 genomes]
rs2692616	0.80[ASN][1000 genomes]
rs2698281	0.82[AMR][1000 genomes]
rs2698283	0.89[ASN][1000 genomes]
rs34097211	0.90[ASN][1000 genomes]
rs34593263	0.87[ASN][1000 genomes]
rs34787881	0.90[ASN][1000 genomes]
rs35043554	0.87[ASN][1000 genomes]
rs35256565	0.90[ASN][1000 genomes]
rs3844090	0.90[AMR][1000 genomes]
rs3924065	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4234662	0.87[ASN][1000 genomes]
rs4485753	0.88[AMR][1000 genomes]
rs4585237	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4629367	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687869	0.87[ASN][1000 genomes]
rs4688021	0.87[ASN][1000 genomes]
rs4688024	0.93[ASN][1000 genomes]
rs524043	0.87[ASN][1000 genomes]
rs525916	0.87[ASN][1000 genomes]
rs540420	0.87[ASN][1000 genomes]
rs56042515	0.88[AMR][1000 genomes]
rs572119	0.91[ASN][1000 genomes]
rs57450016	0.82[AFR][1000 genomes]
rs575833	0.87[ASN][1000 genomes]
rs579196	0.90[ASN][1000 genomes]
rs67683909	0.87[ASN][1000 genomes]
rs6783324	0.87[ASN][1000 genomes]
rs6789941	0.81[ASN][1000 genomes]
rs6790938	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6803814	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68150601	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71325388	0.87[ASN][1000 genomes]
rs71325389	0.86[ASN][1000 genomes]
rs71325397	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73192016	0.82[AFR][1000 genomes]
rs7613825	0.87[ASN][1000 genomes]
rs7626940	0.88[AMR][1000 genomes]
rs8422	0.90[ASN][1000 genomes]
rs940183	0.88[AMR][1000 genomes]
rs9876919	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv1831824	chr3:119263607-119402474	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1014394	chr3:119360506-119412275	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv460834	chr3:119384163-119458851	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv591390	chr3:119384163-119458851	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6792417	COX17	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119356800-119391800	Weak transcription	Brain Substantia Nigra	brain
2	chr3:119356800-119391800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:119358000-119391800	Weak transcription	Colonic Mucosa	Colon
4	chr3:119361200-119394400	Weak transcription	Brain Angular Gyrus	brain
5	chr3:119379200-119391800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:119379200-119392400	Weak transcription	Esophagus	oesophagus
7	chr3:119379200-119392400	Weak transcription	Gastric	stomach
8	chr3:119379800-119391800	Weak transcription	Thymus	Thymus
9	chr3:119380000-119391800	Weak transcription	Lung	lung
10	chr3:119380000-119391800	Weak transcription	Ovary	ovary
11	chr3:119380000-119391800	Weak transcription	Pancreas	Pancrea
12	chr3:119380000-119391800	Weak transcription	Spleen	Spleen
13	chr3:119380000-119392000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:119381000-119392000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr3:119382400-119391800	Weak transcription	Fetal Stomach	stomach
16	chr3:119382600-119391800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr3:119383800-119393800	Strong transcription	Primary B cells from cord blood	blood
18	chr3:119384000-119391800	Weak transcription	HSMMtube	muscle
19	chr3:119384000-119395000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr3:119384200-119391600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr3:119384200-119394400	Weak transcription	Stomach Mucosa	stomach
22	chr3:119384600-119391600	Weak transcription	K562	blood
23	chr3:119384600-119391800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:119384600-119392400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:119384600-119394600	Weak transcription	NH-A	brain
26	chr3:119385200-119392200	Weak transcription	Osteobl	bone
27	chr3:119385400-119394200	Strong transcription	Primary T cells from cord blood	blood
28	chr3:119385400-119394400	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr3:119385600-119394200	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr3:119385600-119394200	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr3:119385600-119394200	Strong transcription	Fetal Thymus	thymus
32	chr3:119385600-119394400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr3:119385600-119394600	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr3:119385800-119394000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr3:119385800-119394000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr3:119385800-119394000	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr3:119386000-119394200	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr3:119386000-119394200	Strong transcription	Placenta	Placenta
39	chr3:119386200-119392000	Weak transcription	NHEK	skin
40	chr3:119386200-119394200	Strong transcription	Dnd41	blood
41	chr3:119386400-119391800	Weak transcription	Left Ventricle	heart
42	chr3:119386400-119394200	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr3:119386400-119394400	Strong transcription	Primary B cells from peripheral blood	blood
44	chr3:119386600-119394200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr3:119387000-119394000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr3:119387000-119394200	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr3:119387400-119392400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:119387400-119392400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr3:119387400-119393800	Strong transcription	Liver	Liver
50	chr3:119387400-119394000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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