Variant report

Variant	rs17316181
Chromosome Location	chr3:139069693-139069694
allele	A/C
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	chr3:139069653-139075359	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:139069612-139071106	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:139069593-139069870	MCF-7	breast:	n/a	n/a
4	POLR2A	chr3:139069687-139069694	HepG2	liver:	n/a	n/a
5	POLR2A	chr3:139069681-139069833	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr3:139069607-139069933	GM12878	blood:	n/a	n/a
7	POLR2A	chr3:139069657-139075279	GM12891	blood:	n/a	n/a
8	POLR2A	chr3:139069579-139081379	K562	blood:	n/a	n/a
9	POLR2A	chr3:139069652-139069718	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:139066912..139069879-chr3:139106229..139109511,3	K562	blood:
2	chr3:139066217..139069193-chr3:139069576..139072044,3	MCF-7	breast:
3	chr3:139069545..139071790-chr3:139077867..139079665,2	MCF-7	breast:

Variant related genes	Relation type
MRPS22	TF binding region
ENSG00000272656	TF binding region
ENSG00000175110	Chromatin interaction
ENSG00000272656	Chromatin interaction
ENSG00000252245	Chromatin interaction
ENSG00000184432	Chromatin interaction
ENSG00000248932	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10513063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1602626	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1602628	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17335312	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17394620	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17395611	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17494356	0.85[ASN][1000 genomes]
rs17560106	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1844977	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2289348	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2289350	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2291555	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2307031	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772876	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs41356949	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs41399544	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55922868	0.90[ASN][1000 genomes]
rs56993164	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57356584	0.89[EUR][1000 genomes]
rs57995350	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58060926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59628512	0.90[ASN][1000 genomes]
rs59958973	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59960641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61034702	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61613889	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61680644	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005158	chr3:139001736-139073011	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv877543	chr3:139021139-139327261	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv4034	chr3:139034976-139080133	Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139063800-139070000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:139064000-139070200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:139064000-139073400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:139064000-139073600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:139064000-139073600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:139064200-139072600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:139064200-139089200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr3:139064400-139097200	Strong transcription	Fetal Muscle Leg	muscle
9	chr3:139064800-139071200	Weak transcription	Fetal Heart	heart
10	chr3:139064800-139074800	Weak transcription	Right Atrium	heart
11	chr3:139064800-139094600	Strong transcription	Primary B cells from cord blood	blood
12	chr3:139065000-139096200	Strong transcription	Fetal Intestine Large	intestine
13	chr3:139065000-139101200	Strong transcription	Primary T cells from cord blood	blood
14	chr3:139065000-139103800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr3:139065000-139103800	Strong transcription	HSMM	muscle
16	chr3:139065000-139104000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:139065200-139073200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:139065200-139073200	Strong transcription	K562	blood
19	chr3:139065200-139089200	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr3:139065200-139093600	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr3:139065200-139096800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr3:139065200-139098000	Strong transcription	Skeletal Muscle Female	skeletal muscle
23	chr3:139065200-139102000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr3:139065200-139102200	Strong transcription	Fetal Muscle Trunk	muscle
25	chr3:139065400-139073800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:139065400-139077000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:139065400-139077600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr3:139065400-139097600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:139065400-139102200	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr3:139065400-139102400	Strong transcription	Duodenum Mucosa	Duodenum
31	chr3:139065400-139102600	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr3:139065400-139102600	Strong transcription	Osteobl	bone
33	chr3:139065400-139103600	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr3:139065400-139103800	Strong transcription	Fetal Thymus	thymus
35	chr3:139065600-139070800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr3:139065600-139070800	Strong transcription	Fetal Stomach	stomach
37	chr3:139065600-139071000	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr3:139065600-139073200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr3:139065600-139077400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr3:139065600-139079600	Strong transcription	Fetal Lung	lung
41	chr3:139065600-139100200	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr3:139065600-139101800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr3:139065600-139102400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr3:139065600-139102400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr3:139065600-139102400	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr3:139065600-139103600	Strong transcription	HUVEC	blood vessel
47	chr3:139065600-139103600	Strong transcription	NH-A	brain
48	chr3:139065600-139103800	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr3:139065600-139103800	Strong transcription	Primary B cells from peripheral blood	blood
50	chr3:139065800-139070800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links