Variant report

Variant	rs2629452
Chromosome Location	chr12:56640886-56640887
allele	C/T
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	chr12:56640835-56641058	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:56613464..56616195-chr12:56639168..56641620,2	MCF-7	breast:
2	chr12:56632924..56644144-chr12:56648283..56654213,19	MCF-7	breast:
3	chr12:56636502..56647526-chr12:56648654..56655042,17	K562	blood:
4	chr12:56637088..56640338-chr12:56640377..56643119,5	K562	blood:

Variant related genes	Relation type
ANKRD52	TF binding region
ENSG00000181852	Chromatin interaction
ENSG00000139645	Chromatin interaction
ENSG00000139579	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1274490	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1274496	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1295772	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17118403	0.84[EUR][1000 genomes]
rs17118409	0.88[EUR][1000 genomes]
rs17118431	0.86[EUR][1000 genomes]
rs17118439	0.83[EUR][1000 genomes]
rs2371454	0.84[EUR][1000 genomes]
rs35526714	0.88[EUR][1000 genomes]
rs59626664	0.88[EUR][1000 genomes]
rs59822547	0.88[EUR][1000 genomes]
rs59917308	0.83[EUR][1000 genomes]
rs60542959	0.81[EUR][1000 genomes]
rs60913149	0.88[EUR][1000 genomes]
rs744051	0.83[EUR][1000 genomes]
rs808919	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs871130	0.84[EUR][1000 genomes]
rs901073	0.86[AFR][1000 genomes]

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	nsv1043622	chr12:56571476-56974448	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv541500	chr12:56571476-56974448	Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2629452	TMEM4	Cis_1M	lymphoblastoid	RTeQTL
rs2629452	RP11-977G19.11	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56624400-56646000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr12:56628600-56644600	Strong transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:56628600-56649800	Strong transcription	Fetal Stomach	stomach
4	chr12:56629000-56649400	Strong transcription	Thymus	Thymus
5	chr12:56629000-56650400	Strong transcription	Rectal Mucosa Donor 29	rectum
6	chr12:56629200-56649600	Strong transcription	Brain Germinal Matrix	brain
7	chr12:56629200-56650000	Strong transcription	Liver	Liver
8	chr12:56629200-56650200	Strong transcription	Brain Anterior Caudate	brain
9	chr12:56629400-56649600	Strong transcription	Fetal Muscle Leg	muscle
10	chr12:56629600-56649600	Strong transcription	Fetal Brain Female	brain
11	chr12:56629800-56649400	Strong transcription	Skeletal Muscle Male	skeletal muscle
12	chr12:56629800-56649800	Strong transcription	Stomach Smooth Muscle	stomach
13	chr12:56629800-56650000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr12:56629800-56650200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:56629800-56650200	Strong transcription	Primary T cells from cord blood	blood
16	chr12:56630000-56643200	Strong transcription	Esophagus	oesophagus
17	chr12:56630000-56644600	Strong transcription	Lung	lung
18	chr12:56630000-56648600	Strong transcription	Dnd41	blood
19	chr12:56630000-56649400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr12:56630000-56649600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr12:56630000-56649600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr12:56630000-56649800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr12:56630000-56650200	Strong transcription	Fetal Muscle Trunk	muscle
24	chr12:56630000-56650600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr12:56630200-56650000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr12:56630400-56644400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr12:56630400-56650200	Strong transcription	Fetal Thymus	thymus
28	chr12:56630600-56650400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr12:56631000-56650000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr12:56631400-56643400	Strong transcription	Brain Cingulate Gyrus	brain
31	chr12:56631800-56649400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr12:56632000-56643400	Strong transcription	Colon Smooth Muscle	Colon
33	chr12:56632200-56650200	Strong transcription	Brain Inferior Temporal Lobe	brain
34	chr12:56632400-56650200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr12:56632600-56643600	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr12:56632600-56650200	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr12:56632600-56650200	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr12:56632800-56649600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr12:56632800-56649600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr12:56632800-56650000	Strong transcription	H9 Cell Line	embryonic stem cell
41	chr12:56632800-56650000	Strong transcription	NHEK	skin
42	chr12:56633000-56643000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr12:56633000-56643400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
44	chr12:56633000-56650000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr12:56633000-56650200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr12:56633000-56650200	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr12:56633000-56650400	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr12:56633000-56650600	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr12:56633200-56649600	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr12:56633200-56650000	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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