Variant report

Variant	rs1779962
Chromosome Location	chr1:247111062-247111063
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:247099451..247101729-chr1:247109483..247112346,2	K562	blood:
2	chr1:247106858..247108880-chr1:247109823..247112372,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1039010	0.82[MEX][hapmap]
rs10924873	0.84[EUR][1000 genomes]
rs10924874	0.80[CHD][hapmap]
rs11579381	0.81[GIH][hapmap]
rs12030390	0.85[EUR][1000 genomes]
rs12075371	0.86[EUR][1000 genomes]
rs12722828	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12730225	0.80[ASN][1000 genomes]
rs12740976	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12750906	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1622905	0.80[EUR][1000 genomes]
rs1691229	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1691230	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1691233	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1691234	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1691244	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1691245	0.81[CEU][hapmap];0.87[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1691246	0.83[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1691250	0.87[JPT][hapmap]
rs1779958	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1779959	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1779960	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1779961	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1779970	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1779985	0.87[JPT][hapmap];0.95[MEX][hapmap];0.81[EUR][1000 genomes]
rs2642977	0.81[MEX][hapmap]
rs2642980	0.85[EUR][1000 genomes]
rs2642982	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2642983	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2642987	0.83[ASN][1000 genomes]
rs2800216	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2800217	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2818887	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55822102	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56217639	0.86[EUR][1000 genomes]
rs6426189	0.83[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6666435	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7410910	0.83[EUR][1000 genomes]
rs7417381	0.90[EUR][1000 genomes]
rs7538195	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs768197	0.82[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers 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	52 gene(s)	inside rSNPs	diseases
4	nsv1011346	chr1:246868799-247133898	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv873424	chr1:246991094-247366380	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
7	nsv1000602	chr1:247044627-247226568	Enhancers Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS 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	30 gene(s)	inside rSNPs	diseases
8	nsv873425	chr1:247069514-247156066	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv873426	chr1:247069514-247162628	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
10	nsv535417	chr1:247094131-247409000	ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
11	nsv1005639	chr1:247094161-247401380	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
12	nsv535418	chr1:247094161-247401380	Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
13	nsv524007	chr1:247098587-247162658	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv1002054	chr1:247108896-247161897	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv535419	chr1:247108896-247161897	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1779962	ZNF695	cis	lymphoblastoid	seeQTL
rs1779962	TRIM58	cis	cerebellum	SCAN
rs1779962	ZNF695	cis	multi-tissue	Pritchard

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247095800-247124800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:247096000-247114600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr1:247096000-247121000	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr1:247096000-247121800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:247096000-247125000	Weak transcription	Brain Germinal Matrix	brain
6	chr1:247096000-247130400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:247096000-247131600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:247096000-247131800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:247096200-247112000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr1:247096200-247112200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr1:247096200-247117400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:247096200-247123000	Weak transcription	K562	blood
13	chr1:247096200-247128400	Weak transcription	Fetal Stomach	stomach
14	chr1:247102400-247123000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr1:247102800-247122000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr1:247103000-247121600	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr1:247106600-247126600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:247107600-247120400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:247107800-247114400	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr1:247107800-247117400	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr1:247107800-247130200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr1:247109600-247115200	Enhancers	Ovary	ovary
23	chr1:247109800-247111200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:247109800-247111400	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr1:247109800-247111400	Enhancers	HUVEC	blood vessel
26	chr1:247109800-247114200	Weak transcription	Dnd41	blood
27	chr1:247110000-247111400	Enhancers	HepG2	liver
28	chr1:247110000-247117400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr1:247110200-247111600	Weak transcription	Aorta	Aorta
30	chr1:247110400-247111200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
31	chr1:247110400-247114400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:247110600-247111200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:247110600-247111200	Active TSS	Brain Anterior Caudate	brain
34	chr1:247110600-247111200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr1:247110600-247111400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:247110600-247111400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:247110600-247111400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr1:247110600-247112400	Enhancers	Adipose Nuclei	Adipose
39	chr1:247110800-247111200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr1:247110800-247111200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:247110800-247112400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
42	chr1:247111000-247111200	Enhancers	Brain Cingulate Gyrus	brain
43	chr1:247111000-247111400	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr1:247111000-247111400	Enhancers	Brain Substantia Nigra	brain
45	chr1:247111000-247111400	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr1:247111000-247111400	Enhancers	HSMM	muscle
47	chr1:247111000-247114600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr1:247111000-247126600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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