Variant report

Variant	rs1274490
Chromosome Location	chr12:56649601-56649602
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:56649574-56649610	MCF-7	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:56648518..56655064-chr12:56657769..56662263,7	K562	blood:
2	chr12:56625950..56631814-chr12:56649549..56655223,8	MCF-7	breast:
3	chr12:56614200..56620176-chr12:56644045..56650698,8	K562	blood:
4	chr12:56613899..56621490-chr12:56648204..56656770,13	K562	blood:
5	chr12:56510333..56513421-chr12:56649218..56653989,6	MCF-7	breast:
6	chr12:56621685..56625461-chr12:56647318..56652615,5	MCF-7	breast:
7	chr12:56632924..56644144-chr12:56648283..56654213,19	MCF-7	breast:
8	chr12:56636502..56647526-chr12:56648654..56655042,17	K562	blood:
9	chr12:56649316..56652198-chr12:56727445..56729500,2	K562	blood:

No data

Variant related genes	Relation type
ANKRD52	TF binding region
ENSG00000135482	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000181852	Chromatin interaction
ENSG00000135469	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000139540	Chromatin interaction
ENSG00000139579	Chromatin interaction
ENSG00000139645	Chromatin interaction
ENSG00000135473	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11171803	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11171806	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11575224	0.82[ASN][1000 genomes]
rs11575229	0.91[ASN][1000 genomes]
rs11575231	0.82[ASN][1000 genomes]
rs11575232	0.82[ASN][1000 genomes]
rs11575234	0.82[ASN][1000 genomes]
rs11575248	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1274493	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1274496	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1295772	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17118403	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17118409	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17118431	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17118439	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2020854	0.87[ASN][1000 genomes]
rs2066807	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2066808	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2066819	0.91[ASN][1000 genomes]
rs2291361	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2306693	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2306694	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2371454	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2371494	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2629447	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2629452	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2643623	0.84[ASN][1000 genomes]
rs2643626	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2695782	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2695788	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2695789	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35526714	0.91[EUR][1000 genomes]
rs41392645	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41423244	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57137641	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57279772	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57343616	0.82[EUR][1000 genomes]
rs57367440	0.82[ASN][1000 genomes]
rs58852079	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59295315	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59626664	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59811639	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59822547	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59917308	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60192809	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60542959	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60913149	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs703830	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs744051	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs773652	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs773664	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs773665	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs808919	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs871130	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs901073	0.88[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
rs1274490	TMEM4	Cis_1M	lymphoblastoid	RTeQTL
rs1274490	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	chr12:56628600-56649800	Strong transcription	Fetal Stomach	stomach
2	chr12:56629000-56650400	Strong transcription	Rectal Mucosa Donor 29	rectum
3	chr12:56629200-56650000	Strong transcription	Liver	Liver
4	chr12:56629200-56650200	Strong transcription	Brain Anterior Caudate	brain
5	chr12:56629800-56649800	Strong transcription	Stomach Smooth Muscle	stomach
6	chr12:56629800-56650000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr12:56629800-56650200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:56629800-56650200	Strong transcription	Primary T cells from cord blood	blood
9	chr12:56630000-56649800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr12:56630000-56650200	Strong transcription	Fetal Muscle Trunk	muscle
11	chr12:56630000-56650600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:56630200-56650000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr12:56630400-56650200	Strong transcription	Fetal Thymus	thymus
14	chr12:56630600-56650400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr12:56631000-56650000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr12:56632200-56650200	Strong transcription	Brain Inferior Temporal Lobe	brain
17	chr12:56632400-56650200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr12:56632600-56650200	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr12:56632600-56650200	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr12:56632800-56650000	Strong transcription	H9 Cell Line	embryonic stem cell
21	chr12:56632800-56650000	Strong transcription	NHEK	skin
22	chr12:56633000-56650000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr12:56633000-56650200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr12:56633000-56650200	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr12:56633000-56650400	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr12:56633000-56650600	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr12:56633200-56650000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr12:56633200-56650600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr12:56633400-56649800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr12:56633400-56650000	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr12:56633400-56650000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr12:56633600-56650600	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr12:56634600-56649800	Strong transcription	NH-A	brain
34	chr12:56634800-56650000	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr12:56634800-56650000	Strong transcription	Rectal Smooth Muscle	rectum
36	chr12:56636800-56650400	Strong transcription	Primary B cells from peripheral blood	blood
37	chr12:56637400-56651400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr12:56638000-56650200	Strong transcription	Hela-S3	cervix
39	chr12:56638200-56650000	Strong transcription	Brain Hippocampus Middle	brain
40	chr12:56638200-56650200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr12:56638200-56650200	Strong transcription	Duodenum Mucosa	Duodenum
42	chr12:56638400-56649800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr12:56638400-56650000	Strong transcription	Adipose Nuclei	Adipose
44	chr12:56638400-56650000	Strong transcription	Placenta Amnion	Placenta Amnion
45	chr12:56638400-56650200	Weak transcription	Right Atrium	heart
46	chr12:56638600-56650000	Strong transcription	Fetal Intestine Large	intestine
47	chr12:56638600-56650200	Strong transcription	Fetal Intestine Small	intestine
48	chr12:56638600-56650200	Strong transcription	Placenta	Placenta
49	chr12:56638600-56650400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr12:56639400-56650000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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