Variant report

Variant	rs12059092
Chromosome Location	chr1:10004608-10004609
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:10004529-10004833	HepG2	liver:	n/a	n/a
2	POLR2A	chr1:10004547-10004741	HepG2	liver:	n/a	n/a
3	POLR2A	chr1:10004581-10004781	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:10002125..10006916-chr1:10090169..10095056,10	K562	blood:
2	chr1:10001502..10006445-chr1:10090966..10096976,9	MCF-7	breast:
3	chr1:9969188..9972816-chr1:10001560..10005397,4	MCF-7	breast:
4	chr1:10002086..10005062-chr1:10091281..10093134,5	K562	blood:
5	chr1:10002061..10004916-chr1:10091716..10094596,6	MCF-7	breast:
6	chr1:9969022..9974825-chr1:10002123..10006220,12	K562	blood:
7	chr1:9968043..9973723-chr1:10001891..10008599,10	K562	blood:
8	chr1:10001294..10005828-chr1:10093316..10096471,4	K562	blood:
9	chr1:10003032..10004962-chr1:10118663..10120416,2	MCF-7	breast:
10	chr1:9881807..9884566-chr1:10002290..10004897,3	K562	blood:
11	chr1:9969199..9972073-chr1:10003014..10005092,3	MCF-7	breast:
12	chr1:9881807..9884566-chr1:10002965..10004897,2	K562	blood:

No data

Variant related genes	Relation type
LZIC	TF binding region
RN7SKP269	TF binding region
ENSG00000178585	Chromatin interaction
ENSG00000130939	Chromatin interaction
ENSG00000171603	Chromatin interaction
ENSG00000233623	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11121501	0.98[AMR][1000 genomes]
rs11121509	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12058979	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12060375	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12062953	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12064822	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12065908	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12070725	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12071307	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12082318	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12086598	0.98[AMR][1000 genomes]
rs12088598	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12094254	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12097182	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17034440	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2289478	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2297843	0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4845912	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4846104	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4846108	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs60132751	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61743470	0.98[AMR][1000 genomes]
rs6663059	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6664208	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7516611	0.93[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7535945	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
2	nsv871610	chr1:9655795-10008221	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv3372906	chr1:9838995-10052992	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv1012469	chr1:9925714-10147796	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv1012301	chr1:9963962-10118393	Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv534853	chr1:9963962-10118393	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv1001742	chr1:9971776-10116767	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
9	nsv1005461	chr1:9972921-10038862	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
10	nsv534855	chr1:9972921-10038862	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
11	nsv947175	chr1:9996275-10009860	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12059092	LZIC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10002400-10004800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:10002400-10004800	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr1:10003800-10004800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
4	chr1:10003800-10004800	Flanking Active TSS	Dnd41	blood
5	chr1:10004000-10004800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr1:10004000-10004800	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr1:10004000-10004800	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr1:10004000-10005200	Enhancers	Spleen	Spleen
9	chr1:10004000-10010600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr1:10004000-10010600	Weak transcription	Fetal Heart	heart
11	chr1:10004000-10034000	Weak transcription	Aorta	Aorta
12	chr1:10004200-10004800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:10004200-10004800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:10004200-10004800	Enhancers	Primary B cells from peripheral blood	blood
15	chr1:10004200-10004800	Enhancers	Primary T cells fromperipheralblood	blood
16	chr1:10004200-10004800	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr1:10004200-10004800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:10004200-10004800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr1:10004200-10004800	Enhancers	Lung	lung
20	chr1:10004200-10004800	Enhancers	Pancreas	Pancrea
21	chr1:10004200-10004800	Flanking Active TSS	Psoas Muscle	Psoas
22	chr1:10004200-10004800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr1:10004200-10005000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr1:10004200-10005200	Enhancers	Adipose Nuclei	Adipose
25	chr1:10004200-10005200	Enhancers	Fetal Muscle Leg	muscle
26	chr1:10004200-10007000	Weak transcription	Fetal Stomach	stomach
27	chr1:10004200-10007200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:10004200-10010000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr1:10004200-10010400	Weak transcription	Fetal Lung	lung
30	chr1:10004200-10010600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr1:10004200-10010600	Weak transcription	Fetal Brain Male	brain
32	chr1:10004200-10010600	Weak transcription	Fetal Kidney	kidney
33	chr1:10004200-10010600	Weak transcription	Ovary	ovary
34	chr1:10004200-10011000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr1:10004200-10019400	Weak transcription	NH-A	brain
36	chr1:10004200-10021000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:10004200-10033800	Weak transcription	Gastric	stomach
38	chr1:10004400-10004800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
39	chr1:10004400-10004800	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr1:10004400-10004800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr1:10004400-10004800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr1:10004400-10004800	Enhancers	Liver	Liver
43	chr1:10004400-10004800	Enhancers	Brain Anterior Caudate	brain
44	chr1:10004400-10004800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr1:10004400-10004800	Enhancers	Colonic Mucosa	Colon
46	chr1:10004400-10004800	Enhancers	Duodenum Mucosa	Duodenum
47	chr1:10004400-10004800	Enhancers	Fetal Muscle Trunk	muscle
48	chr1:10004400-10004800	Enhancers	Left Ventricle	heart
49	chr1:10004400-10004800	Flanking Active TSS	GM12878-XiMat	blood
50	chr1:10004400-10004800	Flanking Active TSS	K562	blood

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