Variant report

Variant	rs1046578
Chromosome Location	chr6:36895835-36895836
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36882284..36884713-chr6:36895663..36897480,2	MCF-7	breast:
2	chr6:36877418..36880214-chr6:36894760..36897203,2	K562	blood:
3	chr6:36895700..36898695-chr6:36952994..36954774,2	MCF-7	breast:
4	chr6:36876919..36878918-chr6:36895703..36897672,2	K562	blood:
5	chr6:36884977..36888283-chr6:36895013..36898238,3	K562	blood:

Variant related genes	Relation type
ENSG00000137409	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1008027	0.80[JPT][hapmap]
rs1022696	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10456446	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10498736	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10947638	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10947639	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10947640	1.00[CEU][hapmap];0.84[CHB][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10947645	1.00[CEU][hapmap];0.84[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10947647	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10947649	0.81[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs11757380	1.00[CEU][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11759850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11963298	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11970506	0.90[EUR][1000 genomes]
rs12110889	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12193721	0.82[EUR][1000 genomes]
rs12194154	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.90[EUR][1000 genomes]
rs12202755	1.00[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12213087	0.90[GIH][hapmap]
rs12213912	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs13199306	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16889252	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2272275	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2272276	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2280675	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293392	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2395663	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3074	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34453243	0.81[ASN][1000 genomes]
rs3734331	0.98[ASN][1000 genomes]
rs3734333	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3957238	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4475317	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4711473	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4711474	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4714023	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59892114	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60992755	0.90[ASN][1000 genomes]
rs6457964	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67854134	0.94[ASN][1000 genomes]
rs6901884	0.94[CEU][hapmap];0.84[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6904504	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6920322	0.91[ASN][1000 genomes]
rs6932038	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6932175	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7741378	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7743646	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7743836	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7757241	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7761425	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7761653	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7770155	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7774420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9296200	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9462238	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9462239	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9462240	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9462241	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9470434	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9470439	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9918461	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9969040	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030015	chr6:36818510-37104446	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv916833	chr6:36826524-37029833	Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1046578	NUDT3	cis	cerebellum	SCAN
rs1046578	C6orf89	cis	parietal	SCAN
rs1046578	PNPLA1	cis	parietal	SCAN
rs1046578	C6orf1	cis	parietal	SCAN
rs1046578	C6orf89	cis	cerebellum	SCAN
rs1046578	KCNK16	cis	parietal	SCAN
rs1046578	SFRS3	cis	lymphoblastoid	GTEx
rs1046578	C6orf89	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36866200-36896400	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr6:36867000-36897000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:36877800-36896000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr6:36880600-36900000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr6:36881400-36896200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr6:36882400-36896800	Weak transcription	Hela-S3	cervix
7	chr6:36884800-36901200	Weak transcription	HMEC	breast
8	chr6:36889400-36897400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:36891600-36901800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr6:36891800-36897800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr6:36892200-36900600	Weak transcription	HUVEC	blood vessel
12	chr6:36892600-36900800	Weak transcription	NHEK	skin
13	chr6:36892800-36896200	Weak transcription	Primary hematopoietic stem cells	blood
14	chr6:36892800-36897400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr6:36892800-36915600	Weak transcription	Pancreas	Pancrea
16	chr6:36893000-36896200	Weak transcription	Spleen	Spleen
17	chr6:36893200-36896800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr6:36893200-36898000	Weak transcription	Esophagus	oesophagus
19	chr6:36893200-36900600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr6:36893400-36897800	Weak transcription	Brain Angular Gyrus	brain
21	chr6:36893600-36896000	Weak transcription	Brain Hippocampus Middle	brain
22	chr6:36893600-36897600	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr6:36893600-36906600	Weak transcription	Thymus	Thymus
24	chr6:36893800-36896000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr6:36893800-36896600	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr6:36893800-36897200	Weak transcription	Primary B cells from cord blood	blood
27	chr6:36893800-36897400	Weak transcription	K562	blood
28	chr6:36893800-36897600	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr6:36893800-36897600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr6:36893800-36898000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr6:36893800-36898400	Weak transcription	Liver	Liver
32	chr6:36893800-36898600	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr6:36893800-36903800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr6:36894000-36897400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr6:36894000-36897400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr6:36894000-36898400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr6:36894000-36898600	Weak transcription	Fetal Brain Female	brain
38	chr6:36894000-36901200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr6:36894200-36897400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr6:36894400-36896800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr6:36894400-36898800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr6:36894400-36899200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr6:36894600-36896200	Enhancers	NHLF	lung
44	chr6:36894600-36897600	Enhancers	Fetal Lung	lung
45	chr6:36894600-36898200	Enhancers	Adipose Nuclei	Adipose
46	chr6:36894600-36898200	Enhancers	HSMM	muscle
47	chr6:36894600-36898200	Enhancers	NHDF-Ad	bronchial
48	chr6:36894600-36898800	Enhancers	Muscle Satellite Cultured Cells	--
49	chr6:36894600-36898800	Enhancers	Ovary	ovary
50	chr6:36894800-36896000	Enhancers	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links