Variant report

Variant	rs6790938
Chromosome Location	chr3:119349989-119349990
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119297851..119299731-chr3:119347893..119350770,2	MCF-7	breast:
2	chr3:119348305..119350713-chr3:119351647..119354186,2	MCF-7	breast:
3	chr3:119298163..119299885-chr3:119348210..119351201,3	MCF-7	breast:
4	chr3:119349377..119351910-chr3:119353160..119355843,2	K562	blood:

Variant related genes	Relation type
ENSG00000242052	Chromatin interaction
ENSG00000272967	Chromatin interaction
ENSG00000144843	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11914676	0.85[ASN][1000 genomes]
rs11923223	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12487499	0.91[ASN][1000 genomes]
rs12488460	0.91[ASN][1000 genomes]
rs12490779	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12492456	0.88[ASN][1000 genomes]
rs1403631	0.86[ASN][1000 genomes]
rs1525836	0.90[ASN][1000 genomes]
rs16830115	0.88[ASN][1000 genomes]
rs16830291	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17203235	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1797827	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1872432	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1985121	0.86[ASN][1000 genomes]
rs2280578	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2670292	0.86[ASN][1000 genomes]
rs2688629	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2688630	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2688631	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2688634	0.89[ASN][1000 genomes]
rs2692616	0.93[ASN][1000 genomes]
rs2698283	0.84[ASN][1000 genomes]
rs34097211	0.88[ASN][1000 genomes]
rs34593263	0.91[ASN][1000 genomes]
rs34787881	0.88[ASN][1000 genomes]
rs35043554	0.91[ASN][1000 genomes]
rs35256565	0.88[ASN][1000 genomes]
rs4234662	0.86[ASN][1000 genomes]
rs4629367	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4687869	0.86[ASN][1000 genomes]
rs4688021	0.86[ASN][1000 genomes]
rs4688024	0.85[ASN][1000 genomes]
rs524043	0.86[ASN][1000 genomes]
rs525916	0.86[ASN][1000 genomes]
rs540420	0.86[ASN][1000 genomes]
rs572119	0.87[ASN][1000 genomes]
rs575833	0.86[ASN][1000 genomes]
rs579196	0.88[ASN][1000 genomes]
rs67683909	0.86[ASN][1000 genomes]
rs6783324	0.86[ASN][1000 genomes]
rs6792417	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6803814	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs68150601	0.82[EUR][1000 genomes]
rs71325388	0.91[ASN][1000 genomes]
rs71325389	0.90[ASN][1000 genomes]
rs7613825	0.91[ASN][1000 genomes]
rs8422	0.88[ASN][1000 genomes]
rs9876919	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv829695	chr3:119178890-119367996	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	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
5	esv1795621	chr3:119344693-119353995	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	esv1795670	chr3:119347400-119353995	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	esv1797032	chr3:119347400-119353995	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	esv1800265	chr3:119347400-119353995	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv591364	chr3:119348130-119353995	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6790938	COX17	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119340800-119357600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:119341400-119364600	Weak transcription	Liver	Liver
3	chr3:119343800-119351400	Enhancers	Psoas Muscle	Psoas
4	chr3:119344400-119351000	Weak transcription	Pancreas	Pancrea
5	chr3:119344600-119352000	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr3:119344800-119350000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:119345000-119350000	Enhancers	Adipose Nuclei	Adipose
8	chr3:119345200-119350800	Weak transcription	Fetal Heart	heart
9	chr3:119345200-119357600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:119345800-119355200	Weak transcription	Brain Hippocampus Middle	brain
11	chr3:119346000-119351400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:119346200-119351000	Enhancers	Muscle Satellite Cultured Cells	--
13	chr3:119346400-119350800	Enhancers	Placenta	Placenta
14	chr3:119346400-119351200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:119346600-119350400	Enhancers	HSMMtube	muscle
16	chr3:119346800-119350600	Enhancers	Osteobl	bone
17	chr3:119346800-119352600	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr3:119347600-119350400	Enhancers	HSMM	muscle
19	chr3:119347800-119350000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr3:119347800-119356400	Weak transcription	Fetal Thymus	thymus
21	chr3:119348200-119350000	Enhancers	GM12878-XiMat	blood
22	chr3:119348800-119350000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr3:119348800-119350200	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr3:119349000-119350000	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr3:119349000-119350000	Enhancers	HUVEC	blood vessel
26	chr3:119349000-119350000	Enhancers	NHDF-Ad	bronchial
27	chr3:119349000-119350000	Enhancers	NHLF	lung
28	chr3:119349000-119350200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr3:119349000-119350600	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr3:119349000-119351200	Enhancers	Rectal Smooth Muscle	rectum
31	chr3:119349000-119351400	Enhancers	K562	blood
32	chr3:119349200-119350000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
33	chr3:119349200-119350000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr3:119349200-119351000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr3:119349400-119350200	Weak transcription	Gastric	stomach
36	chr3:119349400-119350800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:119349400-119351200	Enhancers	Monocytes-CD14+_RO01746	blood
38	chr3:119349400-119351600	Enhancers	Placenta Amnion	Placenta Amnion
39	chr3:119349400-119357600	Weak transcription	Fetal Intestine Small	intestine
40	chr3:119349600-119350000	Enhancers	NH-A	brain
41	chr3:119349600-119354400	Weak transcription	Fetal Stomach	stomach
42	chr3:119349600-119355000	Weak transcription	Spleen	Spleen
43	chr3:119349600-119357000	Weak transcription	Duodenum Mucosa	Duodenum
44	chr3:119349800-119350000	Enhancers	Lung	lung
45	chr3:119349800-119350600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr3:119349800-119350800	Weak transcription	Left Ventricle	heart
47	chr3:119349800-119350800	Weak transcription	Ovary	ovary
48	chr3:119349800-119351000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr3:119349800-119351000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:119349800-119351200	Weak transcription	Colon Smooth Muscle	Colon

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