Variant report

Variant	rs4972529
Chromosome Location	chr2:173952115-173952116
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr2:173952113-173952179	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr2:173951234-173952231	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr2:173952036-173952259	MCF10A-Er-Src	breast:	n/a	n/a
4	TCF12	chr2:173951344-173952123	A549	lung:	n/a	n/a
5	MYC	chr2:173952112-173952276	MCF10A-Er-Src	breast:	n/a	n/a
6	JUND	chr2:173952066-173952164	K562	blood:	n/a	n/a
7	STAT3	chr2:173952089-173952119	MCF10A-Er-Src	breast:	n/a	n/a
8	MAFK	chr2:173952096-173952191	K562	blood:	n/a	n/a
9	STAT3	chr2:173952048-173952259	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:173950777..173953011-chr2:173954741..173957940,3	MCF-7	breast:
2	chr2:173951738..173953586-chr2:173954828..173957652,2	MCF-7	breast:
3	chr2:173944303..173947485-chr2:173950137..173953589,4	MCF-7	breast:
4	chr2:173951489..173953627-chr2:173981191..173983390,3	K562	blood:
5	chr2:173940052..173942648-chr2:173950228..173952997,4	MCF-7	breast:
6	chr2:173938088..173944133-chr2:173944779..173953152,16	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000091436	TF binding region
ENSG00000091436	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11680555	0.82[CEU][hapmap];0.89[JPT][hapmap]
rs11687539	0.89[CEU][hapmap];0.92[JPT][hapmap]
rs12463612	0.88[CEU][hapmap]
rs1551249	0.82[CEU][hapmap]
rs17710065	0.83[CEU][hapmap];0.81[CHB][hapmap];0.92[JPT][hapmap]
rs17710437	0.87[CEU][hapmap];0.92[JPT][hapmap]
rs1809139	0.83[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap]
rs1973037	0.82[CEU][hapmap]
rs2043950	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs3754747	0.88[CEU][hapmap];0.81[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs3754749	0.83[CEU][hapmap]
rs3769159	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs3769162	0.89[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs3769163	0.90[JPT][hapmap]
rs3769201	0.82[CEU][hapmap]
rs3769213	0.82[CEU][hapmap]
rs3820835	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6717529	0.82[CEU][hapmap]
rs6717735	0.82[CEU][hapmap]
rs6742219	0.87[CEU][hapmap]
rs6759847	0.90[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs734993	0.88[CEU][hapmap];0.92[JPT][hapmap]
rs746179	0.88[CEU][hapmap];0.92[JPT][hapmap]
rs7567355	0.90[JPT][hapmap]
rs7599340	0.94[CEU][hapmap]
rs935006	0.94[CEU][hapmap];1.00[JPT][hapmap]
rs935007	0.88[CEU][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4972529	ZAK	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173941600-173955200	Weak transcription	Lung	lung
2	chr2:173941600-173955200	Weak transcription	Pancreas	Pancrea
3	chr2:173941600-173969600	Weak transcription	Spleen	Spleen
4	chr2:173941800-173955200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:173941800-173955200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:173942000-173953000	Weak transcription	Stomach Mucosa	stomach
7	chr2:173942000-173955200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr2:173942000-173955400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr2:173942000-173956000	Weak transcription	Fetal Thymus	thymus
10	chr2:173942600-173956400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr2:173942800-173954800	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr2:173942800-173955800	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr2:173942800-173964600	Weak transcription	HUVEC	blood vessel
14	chr2:173942800-173971400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr2:173943000-173971200	Weak transcription	HSMMtube	muscle
16	chr2:173943200-173955000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr2:173943400-173955200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr2:173943400-173955200	Weak transcription	Dnd41	blood
19	chr2:173943400-173974200	Weak transcription	Fetal Intestine Large	intestine
20	chr2:173943800-173956000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:173945400-173991200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr2:173947000-173955200	Weak transcription	Fetal Muscle Trunk	muscle
23	chr2:173947400-173953200	Enhancers	Liver	Liver
24	chr2:173947600-173954200	Weak transcription	Fetal Intestine Small	intestine
25	chr2:173947600-173955000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr2:173947600-173955200	Weak transcription	Fetal Muscle Leg	muscle
27	chr2:173947600-173955200	Weak transcription	Gastric	stomach
28	chr2:173947600-173955200	Weak transcription	Right Atrium	heart
29	chr2:173948800-173955400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr2:173950400-173953800	Enhancers	Fetal Heart	heart
31	chr2:173950600-173952200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr2:173950600-173952200	Enhancers	Psoas Muscle	Psoas
33	chr2:173951000-173952200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr2:173951000-173952200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr2:173951000-173952200	Enhancers	Adipose Nuclei	Adipose
36	chr2:173951000-173952200	Enhancers	Colon Smooth Muscle	Colon
37	chr2:173951000-173952200	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr2:173951000-173952800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr2:173951000-173952800	Flanking Active TSS	A549	lung
40	chr2:173951000-173953200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:173951000-173953200	Enhancers	Osteobl	bone
42	chr2:173951000-173953400	Enhancers	NHDF-Ad	bronchial
43	chr2:173951200-173952200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:173951200-173952200	Enhancers	Left Ventricle	heart
45	chr2:173951200-173952200	Flanking Active TSS	Stomach Smooth Muscle	stomach
46	chr2:173951200-173952200	Enhancers	HMEC	breast
47	chr2:173951200-173952800	Enhancers	NH-A	brain
48	chr2:173951200-173953000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr2:173951200-173955000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr2:173951200-173955200	Enhancers	Breast Myoepithelial Primary Cells	Breast

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