Variant report

Variant	rs1295772
Chromosome Location	chr12:56628378-56628379
allele	A/G
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:5)
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	chr12:56628235-56634072	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56625950..56631814-chr12:56649549..56655223,8	MCF-7	breast:
2	chr12:56618175..56620748-chr12:56627393..56629347,2	K562	blood:
3	chr12:56627564..56629112-chr12:56636287..56638644,2	K562	blood:
4	chr12:56622344..56625167-chr12:56627296..56629009,2	K562	blood:
5	chr12:56626385..56628815-chr12:56634378..56636026,2	MCF-7	breast:

No data

Variant related genes	Relation type
SLC39A5	TF binding region
ENSG00000139540	Chromatin interaction
ENSG00000139579	Chromatin interaction
ENSG00000139645	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11171803	0.91[ASN][1000 genomes]
rs11171806	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	0.91[ASN][1000 genomes]
rs1274490	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1274493	0.91[ASN][1000 genomes]
rs1274496	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17118403	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17118409	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17118431	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17118439	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2020854	0.87[ASN][1000 genomes]
rs2066807	0.91[ASN][1000 genomes]
rs2066808	0.91[ASN][1000 genomes]
rs2066819	0.91[ASN][1000 genomes]
rs2291361	0.91[ASN][1000 genomes]
rs2306693	0.91[ASN][1000 genomes]
rs2306694	0.91[ASN][1000 genomes]
rs2371454	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2371494	0.91[ASN][1000 genomes]
rs2629447	0.91[ASN][1000 genomes]
rs2629452	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2643623	0.84[ASN][1000 genomes]
rs2643626	0.91[ASN][1000 genomes]
rs2695782	0.91[ASN][1000 genomes]
rs2695788	0.91[ASN][1000 genomes]
rs2695789	0.91[ASN][1000 genomes]
rs35526714	0.91[EUR][1000 genomes]
rs41392645	0.91[ASN][1000 genomes]
rs41423244	0.91[ASN][1000 genomes]
rs57137641	0.91[ASN][1000 genomes]
rs57279772	0.91[ASN][1000 genomes]
rs57343616	0.89[EUR][1000 genomes]
rs57367440	0.82[ASN][1000 genomes]
rs58852079	0.91[ASN][1000 genomes]
rs59295315	0.91[ASN][1000 genomes]
rs59626664	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59811639	0.91[ASN][1000 genomes]
rs59822547	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59917308	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60192809	0.91[ASN][1000 genomes]
rs60542959	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60913149	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs703830	0.91[ASN][1000 genomes]
rs744051	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs773652	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs773664	0.91[ASN][1000 genomes]
rs773665	0.91[ASN][1000 genomes]
rs808919	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs871130	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs901073	0.94[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	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
3	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
rs1295772	TMEM4	Cis_1M	lymphoblastoid	RTeQTL
rs1295772	RP11-977G19.11	cis	Artery Tibial	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56618600-56633800	Weak transcription	Aorta	Aorta
2	chr12:56618800-56628600	Weak transcription	Esophagus	oesophagus
3	chr12:56618800-56629800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:56618800-56629800	Weak transcription	Primary T cells from cord blood	blood
5	chr12:56618800-56630200	Weak transcription	Ovary	ovary
6	chr12:56618800-56630400	Weak transcription	Fetal Thymus	thymus
7	chr12:56618800-56631200	Weak transcription	HSMMtube	muscle
8	chr12:56618800-56633000	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr12:56618800-56633000	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr12:56618800-56634600	Weak transcription	Psoas Muscle	Psoas
11	chr12:56618800-56635200	Weak transcription	Small Intestine	intestine
12	chr12:56618800-56635400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:56618800-56637800	Weak transcription	Fetal Kidney	kidney
14	chr12:56619000-56630400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr12:56619000-56631000	Weak transcription	Primary B cells from peripheral blood	blood
16	chr12:56619000-56632000	Weak transcription	Colon Smooth Muscle	Colon
17	chr12:56619000-56633000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr12:56619000-56633200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr12:56619000-56633400	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr12:56619000-56633600	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr12:56619000-56634000	Weak transcription	Primary B cells from cord blood	blood
22	chr12:56619000-56634800	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr12:56619200-56628600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr12:56619200-56630000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr12:56619200-56630400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:56619200-56631000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr12:56619200-56631200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr12:56619200-56631400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr12:56619200-56632400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr12:56619200-56633000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr12:56619200-56633000	Weak transcription	Primary hematopoietic stem cells	blood
32	chr12:56619200-56633000	Weak transcription	Left Ventricle	heart
33	chr12:56619200-56633400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr12:56619200-56633400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr12:56619200-56634400	Weak transcription	Fetal Lung	lung
36	chr12:56619200-56634600	Weak transcription	HUVEC	blood vessel
37	chr12:56619200-56635000	Weak transcription	HSMM	muscle
38	chr12:56619200-56635400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr12:56619200-56637600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr12:56619400-56629200	Weak transcription	Brain Germinal Matrix	brain
41	chr12:56619400-56629800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr12:56619400-56629800	Weak transcription	Osteobl	bone
43	chr12:56619400-56630000	Weak transcription	A549	lung
44	chr12:56619400-56632600	Weak transcription	NHDF-Ad	bronchial
45	chr12:56619400-56634600	Weak transcription	NH-A	brain
46	chr12:56619400-56637200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr12:56619400-56637800	Weak transcription	Right Atrium	heart
48	chr12:56619600-56629800	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr12:56619600-56632600	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr12:56619600-56634600	Weak transcription	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links