Variant report

Variant	rs57343616
Chromosome Location	chr12:56623347-56623348
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:10)
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	chr12:56623256-56625498	HepG2	liver:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56622689..56625267-chr12:56629999..56633597,3	MCF-7	breast:
2	chr12:56521570..56523702-chr12:56622479..56624701,2	MCF-7	breast:
3	chr12:56621685..56625461-chr12:56647318..56652615,5	MCF-7	breast:
4	chr12:56617919..56620545-chr12:56622814..56625063,4	MCF-7	breast:
5	chr12:56620611..56623587-chr12:56623796..56626645,2	K562	blood:
6	chr12:56582633..56585522-chr12:56623000..56624592,2	MCF-7	breast:
7	chr12:56614920..56617825-chr12:56620846..56625139,7	MCF-7	breast:
8	chr12:56623006..56623578-chr12:56651754..56652640,2	K562	blood:
9	chr12:56614118..56616617-chr12:56622864..56625274,4	K562	blood:
10	chr12:56617987..56620710-chr12:56621012..56624789,4	MCF-7	breast:

No data

Variant related genes	Relation type
SLC39A5	TF binding region
ENSG00000139613	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000258199	Chromatin interaction
ENSG00000139540	Chromatin interaction
ENSG00000258317	Chromatin interaction
ENSG00000181852	Chromatin interaction
ENSG00000139645	Chromatin interaction
ENSG00000139579	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11171803	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11171806	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11575224	0.86[AMR][1000 genomes]
rs11575229	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs11575231	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs11575232	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs11575248	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1274490	0.82[EUR][1000 genomes]
rs1274494	0.80[ASN][1000 genomes]
rs1274496	0.84[EUR][1000 genomes]
rs1295772	0.89[EUR][1000 genomes]
rs17118403	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17118409	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17118431	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17118439	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1802236	1.00[AFR][1000 genomes]
rs2066807	0.82[AMR][1000 genomes]
rs2066818	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2066819	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2069389	1.00[AFR][1000 genomes]
rs2291361	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2306693	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2306694	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2371454	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35526714	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs41392645	0.82[AMR][1000 genomes]
rs41423244	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57137641	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs57279772	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57367440	0.86[AMR][1000 genomes]
rs57870697	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs58852079	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs59295315	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs59626664	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59811639	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs59822547	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs59917308	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs60192809	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs60542959	0.83[EUR][1000 genomes]
rs60913149	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs744051	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs871130	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][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
rs57343616	RP11-977G19.11	cis	Artery Tibial	GTEx
rs57343616	TMEM4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56618600-56633800	Weak transcription	Aorta	Aorta
2	chr12:56618800-56628200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:56618800-56628600	Weak transcription	Esophagus	oesophagus
4	chr12:56618800-56629800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:56618800-56629800	Weak transcription	Primary T cells from cord blood	blood
6	chr12:56618800-56630200	Weak transcription	Ovary	ovary
7	chr12:56618800-56630400	Weak transcription	Fetal Thymus	thymus
8	chr12:56618800-56631200	Weak transcription	HSMMtube	muscle
9	chr12:56618800-56633000	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr12:56618800-56633000	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr12:56618800-56634600	Weak transcription	Psoas Muscle	Psoas
12	chr12:56618800-56635200	Weak transcription	Small Intestine	intestine
13	chr12:56618800-56635400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:56618800-56637800	Weak transcription	Fetal Kidney	kidney
15	chr12:56619000-56623600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr12:56619000-56623600	Strong transcription	Fetal Muscle Trunk	muscle
17	chr12:56619000-56630400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr12:56619000-56631000	Weak transcription	Primary B cells from peripheral blood	blood
19	chr12:56619000-56632000	Weak transcription	Colon Smooth Muscle	Colon
20	chr12:56619000-56633000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr12:56619000-56633200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr12:56619000-56633400	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr12:56619000-56633600	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr12:56619000-56634000	Weak transcription	Primary B cells from cord blood	blood
25	chr12:56619000-56634800	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr12:56619200-56623800	Strong transcription	Fetal Muscle Leg	muscle
27	chr12:56619200-56624400	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr12:56619200-56626800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr12:56619200-56628600	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr12:56619200-56630000	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr12:56619200-56630400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr12:56619200-56631000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr12:56619200-56631200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr12:56619200-56631400	Weak transcription	Brain Cingulate Gyrus	brain
35	chr12:56619200-56632400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr12:56619200-56633000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr12:56619200-56633000	Weak transcription	Primary hematopoietic stem cells	blood
38	chr12:56619200-56633000	Weak transcription	Left Ventricle	heart
39	chr12:56619200-56633400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr12:56619200-56633400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr12:56619200-56634400	Weak transcription	Fetal Lung	lung
42	chr12:56619200-56634600	Weak transcription	HUVEC	blood vessel
43	chr12:56619200-56635000	Weak transcription	HSMM	muscle
44	chr12:56619200-56635400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr12:56619200-56637600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr12:56619400-56623400	Strong transcription	Fetal Stomach	stomach
47	chr12:56619400-56623600	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr12:56619400-56623800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr12:56619400-56623800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr12:56619400-56623800	Strong transcription	Brain Anterior Caudate	brain

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