Variant report

Variant	rs413450
Chromosome Location	chr15:93199313-93199314
allele	G/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	ZNF143	chr15:93198886-93199327	GM12878	blood:	n/a	chr15:93199017-93199027
2	ELF1	chr15:93198312-93199364	MCF-7	breast:	n/a	chr15:93199043-93199052 chr15:93198982-93198991 chr15:93198983-93198995
3	MAX	chr15:93198249-93199577	H1-hESC	embryonic stem cell:	n/a	chr15:93199099-93199109 chr15:93199094-93199104 chr15:93199092-93199101 chr15:93199096-93199105 chr15:93199092-93199107
4	TCF12	chr15:93198781-93199512	A549	lung:	n/a	n/a
5	TCF7L2	chr15:93199060-93199495	PANC-1	pancreas:	n/a	n/a
6	MAX	chr15:93198271-93199489	A549	lung:	n/a	chr15:93199099-93199109 chr15:93199094-93199104 chr15:93199092-93199101 chr15:93199096-93199105 chr15:93199092-93199107
7	MAX	chr15:93198792-93199533	MCF-7	breast:	n/a	chr15:93199099-93199109 chr15:93199094-93199104 chr15:93199092-93199101 chr15:93199096-93199105 chr15:93199092-93199107
8	HDAC2	chr15:93198295-93199446	MCF-7	breast:	n/a	chr15:93198329-93198343
9	SP1	chr15:93198842-93199375	A549	lung:	n/a	chr15:93199100-93199109 chr15:93199099-93199109 chr15:93199098-93199110 chr15:93199098-93199110 chr15:93199099-93199108 chr15:93199099-93199109
10	POLR2A	chr15:93198205-93199327	MCF-7	breast:	n/a	n/a
11	E2F6	chr15:93198346-93199430	A549	lung:	n/a	chr15:93198528-93198540 chr15:93198511-93198520
12	RCOR1	chr15:93198933-93199509	GM12878	blood:	n/a	n/a
13	MTA3	chr15:93198825-93199667	GM12878	blood:	n/a	n/a
14	MXI1	chr15:93198282-93199977	SK-N-SH	brain:	n/a	chr15:93199093-93199102 chr15:93199095-93199104
15	SIN3AK20	chr15:93198616-93199317	PANC-1	pancreas:	n/a	n/a
16	CHD2	chr15:93198930-93199387	GM12878	blood:	n/a	chr15:93199140-93199150
17	SIN3AK20	chr15:93198106-93199396	MCF-7	breast:	n/a	n/a
18	MAX	chr15:93198765-93199445	A549	lung:	n/a	chr15:93199099-93199109 chr15:93199094-93199104 chr15:93199092-93199101 chr15:93199096-93199105 chr15:93199092-93199107
19	USF1	chr15:93198832-93199325	H1-hESC	embryonic stem cell:	n/a	chr15:93198982-93198998
20	E2F6	chr15:93198344-93199394	H1-hESC	embryonic stem cell:	n/a	chr15:93198528-93198540 chr15:93198511-93198520
21	GTF2F1	chr15:93198934-93199350	H1-hESC	embryonic stem cell:	n/a	n/a
22	E2F6	chr15:93198205-93199607	H1-hESC	embryonic stem cell:	n/a	chr15:93198528-93198540 chr15:93198511-93198520
23	POLR2A	chr15:93198358-93199331	H1-neurons	neurons:	n/a	n/a
24	REST	chr15:93197985-93199487	H1-neurons	neurons:	n/a	chr15:93198949-93198969 chr15:93198448-93198461
25	MAX	chr15:93198203-93199479	ECC-1	luminal epithelium:	n/a	chr15:93199099-93199109 chr15:93199094-93199104 chr15:93199092-93199101 chr15:93199096-93199105 chr15:93199092-93199107
26	MAX	chr15:93198284-93199459	ECC-1	luminal epithelium:	n/a	chr15:93199099-93199109 chr15:93199094-93199104 chr15:93199092-93199101 chr15:93199096-93199105 chr15:93199092-93199107
27	TCF12	chr15:93198347-93199382	ECC-1	luminal epithelium:	n/a	chr15:93198411-93198421
28	HA-E2F1	chr15:93198231-93199645	MCF-7	breast:	n/a	chr15:93198528-93198540 chr15:93198511-93198520
29	MAX	chr15:93198228-93199447	MCF-7	breast:	n/a	chr15:93199099-93199109 chr15:93199094-93199104 chr15:93199092-93199101 chr15:93199096-93199105 chr15:93199092-93199107
30	MAX	chr15:93198321-93199427	H1-hESC	embryonic stem cell:	n/a	chr15:93199099-93199109 chr15:93199094-93199104 chr15:93199092-93199101 chr15:93199096-93199105 chr15:93199092-93199107
31	MAX	chr15:93198781-93199454	GM12878	blood:	n/a	chr15:93199099-93199109 chr15:93199094-93199104 chr15:93199092-93199101 chr15:93199096-93199105 chr15:93199092-93199107
32	USF1	chr15:93198787-93199322	ECC-1	luminal epithelium:	n/a	chr15:93198982-93198998
33	MAX	chr15:93198940-93199448	H1-hESC	embryonic stem cell:	n/a	chr15:93199099-93199109 chr15:93199094-93199104 chr15:93199092-93199101 chr15:93199096-93199105 chr15:93199092-93199107

No.	Distal block	Cell Line	Cell type
1	chr15:93188112..93190385-chr15:93199041..93201879,2	K562	blood:
2	chr15:93199083..93200722-chr17:17739000..17741179,2	MCF-7	breast:
3	chr15:93197891..93200562-chr3:14219402..14221003,2	MCF-7	breast:
4	chr15:93187167..93190385-chr15:93197959..93201879,3	K562	blood:

Variant related genes	Relation type
FAM174B	TF binding region
ENSG00000170860	Chromatin interaction
ENSG00000154767	Chromatin interaction
ENSG00000072310	Chromatin interaction
ENSG00000185442	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12443091	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12908852	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1496712	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1496726	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16974307	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2254142	0.89[EUR][1000 genomes]
rs2453901	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs285754	0.87[EUR][1000 genomes]
rs285755	0.88[EUR][1000 genomes]
rs285757	0.88[EUR][1000 genomes]
rs285758	0.88[EUR][1000 genomes]
rs285766	0.80[EUR][1000 genomes]
rs285772	0.90[EUR][1000 genomes]
rs366789	0.82[EUR][1000 genomes]
rs373481	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs406032	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs434826	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs503112	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6496969	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7178546	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs893379	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037972	chr15:92804908-93270761	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv904499	chr15:92914795-93472582	Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	163 gene(s)	inside rSNPs	diseases
3	nsv948738	chr15:93070742-93728147	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv1049490	chr15:93134405-93591660	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
5	nsv1040501	chr15:93177153-93286393	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	esv3374130	chr15:93197573-93200121	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs413450	LOC400451	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93195200-93199600	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr15:93197000-93199600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr15:93197200-93199400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr15:93197200-93199400	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr15:93197200-93199600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr15:93197400-93199400	Flanking Active TSS	Adipose Nuclei	Adipose
7	chr15:93197400-93199600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
8	chr15:93197600-93199400	Active TSS	Pancreas	Pancrea
9	chr15:93197800-93199400	Bivalent/Poised TSS	Brain Germinal Matrix	brain
10	chr15:93197800-93199400	Active TSS	Ovary	ovary
11	chr15:93197800-93199600	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr15:93198000-93199400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
13	chr15:93198000-93199400	Active TSS	Colon Smooth Muscle	Colon
14	chr15:93198000-93199600	Active TSS	Rectal Smooth Muscle	rectum
15	chr15:93198200-93199400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr15:93198200-93199400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
17	chr15:93198200-93199400	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:93198200-93199400	Active TSS	Duodenum Mucosa	Duodenum
19	chr15:93198200-93199400	Bivalent/Poised TSS	A549	lung
20	chr15:93198200-93199400	Active TSS	HSMMtube	muscle
21	chr15:93198200-93199600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr15:93198400-93199400	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr15:93198400-93199400	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr15:93198400-93199400	Active TSS	Aorta	Aorta
25	chr15:93198400-93199400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
26	chr15:93198400-93199400	Bivalent/Poised TSS	Fetal Intestine Large	intestine
27	chr15:93198400-93199400	Active TSS	Fetal Kidney	kidney
28	chr15:93198600-93199400	Active TSS	Primary T helper naive cells from peripheral blood	blood
29	chr15:93198600-93199400	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr15:93198600-93199400	Active TSS	Fetal Muscle Trunk	muscle
31	chr15:93198600-93199400	Bivalent/Poised TSS	Monocytes-CD14+_RO01746	blood
32	chr15:93198800-93199600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
33	chr15:93199000-93199400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
34	chr15:93199000-93199400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr15:93199000-93199400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr15:93199000-93199400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
37	chr15:93199000-93199400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr15:93199000-93199400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
39	chr15:93199000-93199400	Enhancers	Small Intestine	intestine
40	chr15:93199000-93199400	Flanking Active TSS	NH-A	brain
41	chr15:93199000-93199600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr15:93199000-93199600	Flanking Active TSS	Brain Angular Gyrus	brain
43	chr15:93199000-93199600	Flanking Active TSS	Fetal Heart	heart
44	chr15:93199000-93199600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr15:93199000-93199600	Flanking Active TSS	Stomach Smooth Muscle	stomach
46	chr15:93199000-93199600	Flanking Active TSS	GM12878-XiMat	blood
47	chr15:93199000-93200000	Enhancers	Placenta	Placenta
48	chr15:93199200-93199400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr15:93199200-93199400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
50	chr15:93199200-93199400	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links