Variant report

Variant	rs140139
Chromosome Location	chr22:30165412-30165413
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	chr22:30165385-30167411	K562	blood:	n/a	n/a
2	POLR2A	chr22:30165150-30166168	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:30160959..30163738-chr22:30164422..30168687,4	MCF-7	breast:

Variant related genes	Relation type
ZMAT5	TF binding region
ENSG00000184076	Chromatin interaction
ENSG00000100319	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs131267	0.89[EUR][1000 genomes]
rs131268	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs131275	0.84[EUR][1000 genomes]
rs131284	0.94[EUR][1000 genomes]
rs131287	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs131298	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs140114	0.87[EUR][1000 genomes]
rs140117	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs140119	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs140122	0.88[EUR][1000 genomes]
rs140126	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs140127	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs140128	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs140130	0.80[EUR][1000 genomes]
rs140134	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs140140	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs249396	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs249397	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs249401	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs36572	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5752962	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5997534	0.83[ASN][1000 genomes]
rs6006267	0.82[ASN][1000 genomes]
rs737945	0.85[ASN][1000 genomes]
rs7954	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS 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	47 gene(s)	inside rSNPs	diseases
4	esv3455777	chr22:30163399-30165775	Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	esv3427758	chr22:30163408-30165761	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	esv3372672	chr22:30163423-30165783	Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	esv3498901	chr22:30163439-30165723	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	esv3498902	chr22:30163439-30165723	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	esv3455776	chr22:30163466-30165704	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	esv3327609	chr22:30163479-30165716	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	esv3455774	chr22:30163523-30165670	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
12	nsv817987	chr22:30163526-30169436	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	esv3455778	chr22:30163537-30165667	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs140139	MTMR3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30164200-30165600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr22:30164400-30165600	Weak transcription	Primary B cells from peripheral blood	blood
3	chr22:30164400-30165600	Genic enhancers	Fetal Muscle Leg	muscle
4	chr22:30164400-30165800	Weak transcription	Aorta	Aorta
5	chr22:30164400-30166000	Flanking Active TSS	HepG2	liver
6	chr22:30164400-30166400	Weak transcription	Small Intestine	intestine
7	chr22:30164400-30167400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr22:30164600-30165600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr22:30164600-30165600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr22:30164600-30165600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr22:30164600-30165600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr22:30164600-30165600	Weak transcription	Primary B cells from cord blood	blood
13	chr22:30164600-30165600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr22:30164600-30165600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr22:30164600-30165600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr22:30164600-30165600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr22:30164600-30165600	Weak transcription	Esophagus	oesophagus
18	chr22:30164600-30165600	Weak transcription	Fetal Intestine Large	intestine
19	chr22:30164600-30165600	Weak transcription	Gastric	stomach
20	chr22:30164600-30165600	Enhancers	Right Atrium	heart
21	chr22:30164600-30165600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr22:30164600-30165600	Enhancers	Stomach Smooth Muscle	stomach
23	chr22:30164600-30165600	Weak transcription	HSMMtube	muscle
24	chr22:30164600-30165600	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr22:30164600-30165800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr22:30164600-30165800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr22:30164600-30165800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr22:30164600-30165800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
29	chr22:30164600-30165800	Weak transcription	Brain Substantia Nigra	brain
30	chr22:30164600-30165800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr22:30164600-30165800	Weak transcription	Fetal Kidney	kidney
32	chr22:30164600-30166200	Enhancers	Fetal Heart	heart
33	chr22:30164600-30171000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr22:30164600-30183800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr22:30164600-30185000	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr22:30164600-30188600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr22:30164800-30165600	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr22:30164800-30165600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr22:30164800-30167000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr22:30164800-30167200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr22:30164800-30167400	Strong transcription	Fetal Thymus	thymus
42	chr22:30164800-30167600	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr22:30165000-30165600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr22:30165000-30165600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr22:30165000-30165600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr22:30165000-30165600	Weak transcription	Brain Anterior Caudate	brain
47	chr22:30165000-30165800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr22:30165000-30165800	Weak transcription	HMEC	breast
49	chr22:30165000-30166800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
50	chr22:30165000-30167000	Strong transcription	HUES48 Cell Line	embryonic stem cell

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