Variant report

Variant	rs1360780
Chromosome Location	chr6:35607571-35607572
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:35606015..35609857-chr6:35612357..35615578,3	K562	blood:
2	chr6:35605150..35607855-chr6:35700616..35702117,2	K562	blood:
3	chr6:35465446..35468035-chr6:35607430..35610345,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12055438	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1591365	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2395634	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3798347	1.00[CEU][hapmap];0.93[CHB][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3800372	0.85[EUR][1000 genomes]
rs3800373	0.88[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];0.84[LWK][hapmap];0.89[MEX][hapmap];0.82[MKK][hapmap];0.85[TSI][hapmap];0.89[YRI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4713904	0.87[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.85[ASN][1000 genomes]
rs4713906	0.85[ASN][1000 genomes]
rs6457836	0.81[CHD][hapmap]
rs6902124	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6931118	0.84[EUR][1000 genomes]
rs7751598	0.88[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9296158	0.85[CEU][hapmap];0.93[CHB][hapmap];0.99[EUR][1000 genomes]
rs9296159	0.82[EUR][1000 genomes]
rs9357201	0.85[EUR][1000 genomes]
rs9357202	0.86[EUR][1000 genomes]
rs9368878	0.88[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];1.00[EUR][1000 genomes]
rs9368881	0.85[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs9368885	0.85[EUR][1000 genomes]
rs9380522	0.82[EUR][1000 genomes]
rs9380525	0.85[CEU][hapmap];0.82[CHB][hapmap];0.86[EUR][1000 genomes]
rs9380526	0.85[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs9394309	0.93[GIH][hapmap];0.90[TSI][hapmap]
rs943297	0.88[GIH][hapmap];0.86[TSI][hapmap]
rs9462104	0.81[TSI][hapmap]
rs9470080	0.81[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758048	chr6:35463741-35806504	Genic enhancers Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2759420	chr6:35463741-35806504	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv517211	chr6:35502202-35607571	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv602924	chr6:35505311-35750299	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv885801	chr6:35537406-35671651	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	esv3430300	chr6:35549151-35959004	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	esv1812273	chr6:35597703-35629285	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv5258	chr6:35601724-35658344	Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
9	nsv821646	chr6:35604428-35802594	Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
10	esv1848884	chr6:35607571-35629669	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1360780	MDGA1	cis	cerebellum	SCAN
rs1360780	BAK1	cis	cerebellum	SCAN
rs1360780	ANKS1A	cis	cerebellum	SCAN
rs1360780	BRPF3	cis	cerebellum	SCAN
rs1360780	FKBP5	Cis_1M	lymphoblastoid	RTeQTL
rs1360780	HMGA1	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35570200-35608600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr6:35570800-35611400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:35571200-35611800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr6:35575000-35611600	Strong transcription	Liver	Liver
5	chr6:35575600-35610400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr6:35577600-35613200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr6:35583200-35608000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr6:35584200-35607600	Weak transcription	Primary B cells from peripheral blood	blood
9	chr6:35585600-35610800	Weak transcription	Fetal Muscle Leg	muscle
10	chr6:35585800-35607800	Weak transcription	Colon Smooth Muscle	Colon
11	chr6:35586800-35613800	Weak transcription	Fetal Stomach	stomach
12	chr6:35587000-35607800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr6:35587000-35607800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:35588000-35608400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr6:35588200-35630800	Weak transcription	Colonic Mucosa	Colon
16	chr6:35589000-35607800	Weak transcription	NHDF-Ad	bronchial
17	chr6:35592000-35610200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr6:35592000-35611400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr6:35592800-35612000	Weak transcription	HepG2	liver
20	chr6:35594200-35614800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:35594600-35614600	Strong transcription	Fetal Thymus	thymus
22	chr6:35594800-35610600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr6:35597000-35608400	Weak transcription	Fetal Kidney	kidney
24	chr6:35597000-35615400	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr6:35597400-35613000	Strong transcription	K562	blood
26	chr6:35597600-35611800	Strong transcription	Left Ventricle	heart
27	chr6:35597800-35614200	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr6:35600000-35607800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr6:35600000-35611200	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr6:35600200-35610400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:35600800-35607800	Strong transcription	NHEK	skin
32	chr6:35601000-35611400	Strong transcription	Thymus	Thymus
33	chr6:35601400-35612000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
34	chr6:35602000-35609600	Strong transcription	Stomach Smooth Muscle	stomach
35	chr6:35602000-35613600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr6:35602200-35611400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr6:35602400-35610600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr6:35602600-35607800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr6:35602600-35607800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr6:35602600-35607800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr6:35602600-35607800	Weak transcription	Fetal Heart	heart
42	chr6:35602600-35610400	Weak transcription	Fetal Intestine Large	intestine
43	chr6:35602600-35610800	Weak transcription	NHLF	lung
44	chr6:35602600-35612000	Weak transcription	Stomach Mucosa	stomach
45	chr6:35602800-35608800	Weak transcription	Placenta	Placenta
46	chr6:35602800-35612000	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr6:35603000-35609400	Strong transcription	Duodenum Mucosa	Duodenum
48	chr6:35603000-35610600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr6:35603200-35607800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr6:35603400-35608000	Genic enhancers	Primary T helper cells fromperipheralblood	blood

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