Variant report

Variant	rs7539282
Chromosome Location	chr1:227950111-227950112
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:227668951..227669884-chr1:227949577..227950975,4	MCF-7	breast:
2	chr1:227946182..227953403-chr1:228132950..228136592,12	MCF-7	breast:
3	chr1:227949872..227950667-chr1:228129639..228130594,3	MCF-7	breast:
4	chr1:227945386..227947892-chr1:227948405..227951247,3	MCF-7	breast:
5	chr1:227948959..227950844-chr1:228133923..228134938,14	MCF-7	breast:
6	chr1:227913567..227919162-chr1:227947935..227954215,6	MCF-7	breast:
7	chr1:227949868..227950613-chr1:228089588..228090311,2	K562	blood:
8	chr1:227932601..227934786-chr1:227948065..227950535,2	MCF-7	breast:
9	chr1:227949923..227950798-chr1:228261303..228262101,2	K562	blood:
10	chr1:227948352..227950485-chr1:227952945..227955700,2	MCF-7	breast:
11	chr1:227636541..227637330-chr1:227949858..227950651,2	K562	blood:
12	chr1:227948805..227951027-chr1:227953567..227955861,2	MCF-7	breast:
13	chr1:227948596..227951213-chr1:228129640..228131293,2	MCF-7	breast:
14	chr1:227918162..227918668-chr1:227949863..227950566,2	MCF-7	breast:
15	chr1:227948253..227951244-chr1:228133555..228136345,5	MCF-7	breast:
16	chr1:227950090..227952610-chr1:228122891..228125327,3	MCF-7	breast:
17	chr1:227938992..227942354-chr1:227946217..227950282,3	K562	blood:
18	chr1:227949885..227950870-chr1:228141682..228142414,6	K562	blood:
19	chr1:227949835..227950876-chr1:228133993..228134931,7	K562	blood:
20	chr1:227949805..227950774-chr1:227975453..227976341,2	K562	blood:
21	chr1:227949947..227950738-chr17:18770247..18771173,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000143816	Chromatin interaction
ENSG00000143740	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1056699	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1060295	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10799430	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs10799439	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10799447	0.82[CEU][hapmap];0.80[TSI][hapmap]
rs10916171	0.92[CEU][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs10916188	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10916191	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10916203	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916207	0.82[CEU][hapmap];0.80[TSI][hapmap]
rs1111046	0.89[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1155807	0.96[CEU][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12025942	0.92[CEU][hapmap]
rs1810680	0.96[CEU][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1923823	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2104245	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2236360	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2236361	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4500311	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4653856	0.92[CEU][hapmap];0.80[JPT][hapmap]
rs6426468	0.96[CEU][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6426473	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6660432	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6693054	0.96[CEU][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6703846	0.96[CEU][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs730684	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7522634	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7526184	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533588	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7534403	0.96[CEU][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7536765	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7552193	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9786978	0.92[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9969994	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][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	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
5	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
6	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
7	nsv515496	chr1:227912474-227967938	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS 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	28 gene(s)	inside rSNPs	diseases
8	nsv873249	chr1:227920061-228121548	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv468238	chr1:227935762-228045748	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS 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	9 gene(s)	inside rSNPs	diseases
10	nsv549272	chr1:227935762-228045748	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7539282	ZNF678	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227924200-227955000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:227934800-227950200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:227934800-227950400	Strong transcription	Fetal Intestine Small	intestine
4	chr1:227938000-227950200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:227938600-227950400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr1:227944000-227950400	Strong transcription	Fetal Intestine Large	intestine
7	chr1:227944000-227951800	Genic enhancers	Fetal Muscle Leg	muscle
8	chr1:227945800-227954800	Weak transcription	Fetal Kidney	kidney
9	chr1:227946000-227950600	Genic enhancers	GM12878-XiMat	blood
10	chr1:227946000-227960400	Strong transcription	Fetal Brain Female	brain
11	chr1:227946800-227952400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:227947600-227954800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr1:227947800-227950200	Strong transcription	Ovary	ovary
14	chr1:227947800-227950400	Weak transcription	HUVEC	blood vessel
15	chr1:227947800-227951600	Enhancers	Fetal Heart	heart
16	chr1:227947800-227955400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr1:227948000-227950400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:227948000-227950400	Strong transcription	Fetal Stomach	stomach
19	chr1:227948000-227953600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr1:227948200-227952200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
21	chr1:227948200-227954600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr1:227948400-227955400	Weak transcription	Psoas Muscle	Psoas
23	chr1:227948400-227956000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr1:227948600-227950200	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
25	chr1:227948600-227955600	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr1:227948800-227952800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr1:227949000-227950200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:227949000-227950400	Strong transcription	NHLF	lung
29	chr1:227949000-227953400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr1:227949200-227951000	Enhancers	Rectal Mucosa Donor 29	rectum
31	chr1:227949200-227951200	Genic enhancers	Colonic Mucosa	Colon
32	chr1:227949200-227951200	Genic enhancers	Gastric	stomach
33	chr1:227949200-227951800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr1:227949200-227952200	Genic enhancers	Esophagus	oesophagus
35	chr1:227949200-227954400	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr1:227949200-227954800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr1:227949200-227956000	Genic enhancers	Fetal Thymus	thymus
38	chr1:227949400-227950200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:227949400-227950200	Weak transcription	Fetal Brain Male	brain
40	chr1:227949400-227950400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:227949400-227950400	Genic enhancers	Spleen	Spleen
42	chr1:227949400-227950600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr1:227949400-227952200	Genic enhancers	Fetal Muscle Trunk	muscle
44	chr1:227949400-227954200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr1:227949400-227954400	Enhancers	Placenta Amnion	Placenta Amnion
46	chr1:227949400-227954600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr1:227949600-227950200	Weak transcription	Primary B cells from cord blood	blood
48	chr1:227949600-227950200	Genic enhancers	Primary hematopoietic stem cells	blood
49	chr1:227949600-227950200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:227949600-227950400	Weak transcription	Primary monocytes fromperipheralblood	blood

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