Variant report

Variant	rs6663178
Chromosome Location	chr1:184661642-184661643
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:184660734..184663432-chr1:184719379..184720906,2	MCF-7	breast:
2	chr1:184355848..184357753-chr1:184661585..184663546,2	MCF-7	breast:
3	chr1:184657884..184659599-chr1:184661545..184663873,2	K562	blood:
4	chr1:184019721..184021279-chr1:184661533..184663117,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198860	Chromatin interaction
ENSG00000116667	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1040666	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1046239	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1061508	0.92[CEU][hapmap];0.89[GIH][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs10752941	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10797987	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10911640	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10911644	0.81[GIH][hapmap]
rs12032144	0.83[EUR][1000 genomes]
rs12043236	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12071631	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12124714	0.82[EUR][1000 genomes]
rs12124929	0.85[GIH][hapmap]
rs12133674	0.92[EUR][1000 genomes]
rs12567225	0.85[GIH][hapmap]
rs12567226	0.85[GIH][hapmap]
rs2024764	0.81[EUR][1000 genomes]
rs2024765	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2024766	0.81[EUR][1000 genomes]
rs2024767	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2207733	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2333715	0.85[GIH][hapmap]
rs2333716	0.96[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35478695	0.82[EUR][1000 genomes]
rs3736757	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3895196	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.89[ASN][1000 genomes]
rs4469687	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4498770	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4651230	0.83[GIH][hapmap]
rs6677073	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs726427	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs7523023	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7525074	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs861575	0.94[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs861577	0.83[ASN][1000 genomes]
rs861578	0.89[GIH][hapmap]
rs861579	0.88[ASN][1000 genomes]
rs861581	0.89[GIH][hapmap]
rs861582	0.89[ASN][1000 genomes]
rs9425339	0.82[ASN][1000 genomes]
rs9425341	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9425343	0.85[GIH][hapmap]
rs9425633	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9425634	0.84[EUR][1000 genomes]
rs9425635	0.85[EUR][1000 genomes]
rs9658937	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9661314	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs971080	0.82[EUR][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	esv2756618	chr1:184393343-184674343	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	nsv832037	chr1:184568194-184756597	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv917126	chr1:184655366-184902273	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv832048	chr1:184660146-184858802	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6663178	EDEM3	cis	Nerve Tibial	GTEx
rs6663178	PTRF	trans	cerebellum	SCAN
rs6663178	EDEM3	cis	Esophagus Muscularis	GTEx
rs6663178	EDEM3	Cis_1M	lymphoblastoid	RTeQTL
rs6663178	EDEM3	cis	Artery Tibial	GTEx
rs6663178	PRG4	cis	parietal	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184641400-184672800	Weak transcription	Gastric	stomach
2	chr1:184649400-184662800	Weak transcription	Osteobl	bone
3	chr1:184653200-184705000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:184653800-184662000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:184654000-184662200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:184654000-184662200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr1:184654000-184662200	Weak transcription	Left Ventricle	heart
8	chr1:184654000-184662800	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr1:184654000-184710800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:184654200-184662200	Weak transcription	Brain Angular Gyrus	brain
11	chr1:184654200-184662200	Weak transcription	Psoas Muscle	Psoas
12	chr1:184654200-184662200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr1:184654200-184662200	Weak transcription	NHDF-Ad	bronchial
14	chr1:184654200-184662400	Weak transcription	Colon Smooth Muscle	Colon
15	chr1:184654200-184662600	Weak transcription	Ovary	ovary
16	chr1:184654200-184672000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr1:184654200-184701200	Weak transcription	Stomach Mucosa	stomach
18	chr1:184654200-184710000	Weak transcription	Esophagus	oesophagus
19	chr1:184654400-184662000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr1:184654400-184662200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:184654400-184662200	Weak transcription	Adipose Nuclei	Adipose
22	chr1:184654400-184662200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr1:184654400-184662400	Weak transcription	Brain Hippocampus Middle	brain
24	chr1:184654400-184675400	Weak transcription	Pancreas	Pancrea
25	chr1:184654600-184662000	Weak transcription	Primary B cells from peripheral blood	blood
26	chr1:184654600-184662200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:184654600-184665800	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr1:184654600-184672400	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr1:184654800-184662400	Weak transcription	Placenta	Placenta
30	chr1:184654800-184669600	Weak transcription	Fetal Lung	lung
31	chr1:184655000-184662200	Weak transcription	GM12878-XiMat	blood
32	chr1:184655000-184664400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr1:184655800-184663200	Weak transcription	Brain Germinal Matrix	brain
34	chr1:184656000-184661800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:184656000-184672000	Weak transcription	HepG2	liver
36	chr1:184656200-184662200	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr1:184656400-184672800	Weak transcription	Spleen	Spleen
38	chr1:184656600-184662200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr1:184656600-184662200	Weak transcription	HSMMtube	muscle
40	chr1:184656600-184670200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:184656600-184684000	Weak transcription	Fetal Heart	heart
42	chr1:184656800-184662200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr1:184657000-184672600	Weak transcription	Lung	lung
44	chr1:184657200-184662400	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr1:184657200-184672800	Weak transcription	Fetal Intestine Small	intestine
46	chr1:184657400-184672800	Weak transcription	Fetal Stomach	stomach
47	chr1:184657600-184662000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:184657800-184662000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr1:184657800-184662000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr1:184657800-184670200	Weak transcription	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links