Variant report

Variant	rs11687539
Chromosome Location	chr2:174023857-174023858
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:174023230-174026672	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr2:174023821-174023860	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr2:174022251-174026716	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr2:174023824-174024048	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000091436	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11680555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[AFR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12463612	0.87[CEU][hapmap]
rs13004345	0.88[YRI][hapmap]
rs1551249	0.83[CEU][hapmap]
rs17710065	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17710437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1809139	0.94[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1837470	0.88[YRI][hapmap]
rs1973037	0.83[CEU][hapmap]
rs2043950	0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2358088	0.88[ASN][1000 genomes]
rs3754739	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3754747	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs3754749	0.83[CEU][hapmap]
rs3769159	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3769162	0.89[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3769163	1.00[JPT][hapmap];0.87[YRI][hapmap];0.97[AFR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3769173	0.85[ASN][1000 genomes]
rs3769184	0.89[YRI][hapmap]
rs3769201	0.82[CEU][hapmap]
rs3769213	0.83[CEU][hapmap]
rs3820835	0.89[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap]
rs4399689	0.97[AFR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4972529	0.89[CEU][hapmap];0.92[JPT][hapmap]
rs4972532	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56980119	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59500540	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61264428	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62175824	0.92[AFR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6433392	0.85[CEU][hapmap]
rs6717529	0.83[CEU][hapmap]
rs6717735	0.83[CEU][hapmap]
rs6742219	0.87[CEU][hapmap]
rs6759847	0.91[CHB][hapmap];0.92[JPT][hapmap]
rs722864	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs734993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73974105	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs746179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7567355	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7575319	0.97[AFR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7599340	0.94[CEU][hapmap]
rs7601536	0.97[AFR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs935006	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs935007	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011724	chr2:173916482-174231908	Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv834460	chr2:173919464-174085288	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv834461	chr2:173979734-174038471	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11687539	ZAK	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:174012800-174026600	Enhancers	Skeletal Muscle Female	skeletal muscle
2	chr2:174013400-174025400	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr2:174013600-174024600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr2:174015400-174027400	Weak transcription	Fetal Muscle Leg	muscle
5	chr2:174015400-174047000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr2:174016200-174048800	Weak transcription	K562	blood
7	chr2:174016400-174028200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:174017200-174024000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr2:174017200-174024200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr2:174018000-174024200	Weak transcription	Fetal Heart	heart
11	chr2:174018000-174025400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:174018400-174024000	Weak transcription	Osteobl	bone
13	chr2:174018400-174024200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr2:174018600-174024200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr2:174021200-174024800	Weak transcription	Primary hematopoietic stem cells	blood
16	chr2:174021600-174024200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:174021600-174024200	Weak transcription	Ovary	ovary
18	chr2:174021600-174025600	Weak transcription	Fetal Intestine Small	intestine
19	chr2:174021600-174027000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr2:174021600-174027800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr2:174021600-174030400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr2:174021800-174025400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr2:174021800-174026400	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr2:174022000-174024800	Weak transcription	Right Ventricle	heart
25	chr2:174022000-174027800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr2:174022200-174024400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:174022400-174024200	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr2:174022400-174024400	Enhancers	A549	lung
29	chr2:174022400-174024400	Enhancers	Hela-S3	cervix
30	chr2:174022400-174025400	Enhancers	NHDF-Ad	bronchial
31	chr2:174022400-174026400	Enhancers	NHEK	skin
32	chr2:174022400-174026600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr2:174022400-174026600	Enhancers	HMEC	breast
34	chr2:174022600-174024200	Weak transcription	Adipose Nuclei	Adipose
35	chr2:174022600-174025400	Weak transcription	Left Ventricle	heart
36	chr2:174022600-174025400	Weak transcription	Psoas Muscle	Psoas
37	chr2:174022800-174024200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr2:174022800-174024200	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr2:174023200-174024400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr2:174023200-174024400	Weak transcription	Colon Smooth Muscle	Colon
41	chr2:174023600-174025400	Weak transcription	Aorta	Aorta
42	chr2:174023800-174024200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr2:174023800-174024400	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr2:174023800-174024800	Enhancers	NHLF	lung
45	chr2:174023800-174026600	Enhancers	Primary monocytes fromperipheralblood	blood

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