Variant report

Variant	rs2358538
Chromosome Location	chr12:50586627-50586628
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	EP300	chr12:50586610-50586909	SK-N-SH_RA	brain:	n/a	n/a
2	PBX3	chr12:50586526-50587209	SK-N-SH	brain:	n/a	n/a
3	NFIC	chr12:50586483-50587119	SK-N-SH	brain:	n/a	n/a
4	GATA3	chr12:50586556-50587122	SK-N-SH	brain:	n/a	chr12:50586861-50586874
5	EP300	chr12:50586443-50587237	SK-N-SH	brain:	n/a	n/a
6	TCF12	chr12:50586488-50587261	SK-N-SH	brain:	n/a	chr12:50586952-50586961
7	MAX	chr12:50586602-50587117	SK-N-SH	brain:	n/a	n/a
8	GATA3	chr12:50586449-50587248	SK-N-SH	brain:	n/a	chr12:50586861-50586874
9	FOSL2	chr12:50586514-50587251	SK-N-SH	brain:	n/a	n/a
10	TCF12	chr12:50586457-50587227	SK-N-SH	brain:	n/a	chr12:50586952-50586961
11	JUND	chr12:50586567-50587193	SK-N-SH	brain:	n/a	n/a
12	CHD1	chr12:50586305-50587274	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:50580197..50581923-chr12:50586405..50588102,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257298	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1044370	0.81[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.86[MKK][hapmap];0.81[TSI][hapmap];0.83[YRI][hapmap];0.90[ASN][1000 genomes]
rs10747573	0.85[GIH][hapmap]
rs10783342	0.89[ASW][hapmap];0.97[GIH][hapmap];0.84[TSI][hapmap]
rs11169294	0.81[ASN][1000 genomes]
rs11831413	0.83[ASN][1000 genomes]
rs12426261	0.89[ASN][1000 genomes]
rs12815871	0.81[ASN][1000 genomes]
rs12830386	0.83[ASN][1000 genomes]
rs1362984	0.87[EUR][1000 genomes]
rs1862042	0.85[EUR][1000 genomes]
rs1862043	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2178173	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs34573394	0.83[ASN][1000 genomes]
rs35549836	0.83[ASN][1000 genomes]
rs35998534	0.83[ASN][1000 genomes]
rs4459386	1.00[ASW][hapmap];0.97[GIH][hapmap];0.83[MKK][hapmap];0.84[TSI][hapmap];0.80[YRI][hapmap]
rs4883481	0.98[ASN][1000 genomes]
rs4883482	0.92[ASN][1000 genomes]
rs56709084	0.83[ASN][1000 genomes]
rs646782	1.00[CHB][hapmap]
rs6580729	0.81[ASW][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6580734	0.83[EUR][1000 genomes]
rs66768395	0.88[ASN][1000 genomes]
rs706791	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs706792	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs706793	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7136570	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs7136648	0.87[EUR][1000 genomes]
rs7279	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs7294548	0.83[ASN][1000 genomes]
rs7297421	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs7301566	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7301649	0.83[ASN][1000 genomes]
rs7302981	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.90[YRI][hapmap]
rs7308356	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7308692	0.86[EUR][1000 genomes]
rs7309519	0.83[EUR][1000 genomes]
rs7532	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7957659	1.00[ASW][hapmap];0.97[GIH][hapmap];0.81[MKK][hapmap];0.84[TSI][hapmap];0.80[YRI][hapmap]
rs7967954	0.89[ASW][hapmap];0.97[GIH][hapmap];0.84[TSI][hapmap]
rs8181679	0.89[ASW][hapmap];0.97[GIH][hapmap];0.80[MKK][hapmap];0.84[TSI][hapmap]
rs836172	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs836177	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs836179	1.00[CHB][hapmap]
rs836180	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs860698	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9668955	0.85[EUR][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	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2358538	LASS5	cis	cerebellum	SCAN
rs2358538	KIAA1463	cis	multi-tissue	Pritchard
rs2358538	LASS5	cis	parietal	SCAN
rs2358538	DIP2B	cis	cerebellum	SCAN
rs2358538	FAM186B	cis	parietal	SCAN
rs2358538	MCRS1	cis	parietal	SCAN
rs2358538	LASS5	cis	multi-tissue	Pritchard
rs2358538	CERS5	cis	Nerve Tibial	GTEx
rs2358538	SLC38A4	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50562200-50597000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr12:50564400-50600800	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr12:50570000-50601400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:50570400-50592800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr12:50570800-50589800	Strong transcription	Fetal Stomach	stomach
6	chr12:50571800-50595800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr12:50571800-50597000	Weak transcription	Thymus	Thymus
8	chr12:50571800-50597600	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr12:50571800-50614200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:50572200-50614000	Weak transcription	Right Ventricle	heart
11	chr12:50576600-50595000	Weak transcription	A549	lung
12	chr12:50579600-50598000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr12:50580400-50595800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr12:50581800-50601000	Weak transcription	Brain Substantia Nigra	brain
15	chr12:50582000-50592000	Weak transcription	Fetal Kidney	kidney
16	chr12:50582000-50596000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr12:50582400-50596200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr12:50582400-50598200	Weak transcription	Brain Hippocampus Middle	brain
19	chr12:50582400-50600000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr12:50582600-50589200	Strong transcription	Fetal Muscle Trunk	muscle
21	chr12:50582600-50593000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr12:50582600-50597000	Weak transcription	Fetal Brain Female	brain
23	chr12:50582600-50598000	Weak transcription	Psoas Muscle	Psoas
24	chr12:50582600-50598200	Weak transcription	Pancreas	Pancrea
25	chr12:50582800-50589000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr12:50582800-50592000	Weak transcription	Spleen	Spleen
27	chr12:50582800-50592600	Weak transcription	Fetal Brain Male	brain
28	chr12:50582800-50614000	Weak transcription	Brain Angular Gyrus	brain
29	chr12:50582800-50614200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr12:50583000-50592800	Weak transcription	Esophagus	oesophagus
31	chr12:50583000-50592800	Weak transcription	Gastric	stomach
32	chr12:50583000-50594200	Weak transcription	Ovary	ovary
33	chr12:50583000-50614400	Weak transcription	Brain Anterior Caudate	brain
34	chr12:50583200-50589200	Strong transcription	Fetal Muscle Leg	muscle
35	chr12:50583200-50592800	Weak transcription	Small Intestine	intestine
36	chr12:50583400-50587200	Strong transcription	HMEC	breast
37	chr12:50583400-50598200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr12:50583400-50600800	Strong transcription	Adipose Nuclei	Adipose
39	chr12:50583600-50587200	Strong transcription	NHEK	skin
40	chr12:50583600-50591800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr12:50584000-50586800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr12:50584000-50587200	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr12:50584400-50587000	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr12:50584400-50587000	Genic enhancers	Fetal Intestine Large	intestine
45	chr12:50584600-50586800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr12:50584600-50586800	Strong transcription	Primary T cells from cord blood	blood
47	chr12:50584600-50586800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr12:50584600-50587000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr12:50584600-50587000	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr12:50584600-50587000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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