Variant report

Variant	rs1376178
Chromosome Location	chr5:40908901-40908902
allele	A/C
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	MXI1	chr5:40908860-40910989	SK-N-SH	brain:	n/a	n/a
2	EP300	chr5:40908721-40911081	SK-N-SH	brain:	n/a	chr5:40910080-40910094 chr5:40909927-40909936 chr5:40910078-40910092 chr5:40910077-40910091 chr5:40910079-40910093
3	GATA3	chr5:40908901-40909464	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:40906764..40908944-chr5:40910686..40913310,2	K562	blood:

Variant related genes	Relation type
C7	TF binding region
ENSG00000253098	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10067114	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10071209	0.97[ASN][1000 genomes]
rs10472345	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1063499	0.89[EUR][1000 genomes]
rs1376180	0.93[EUR][1000 genomes]
rs1376181	0.93[EUR][1000 genomes]
rs1697938	0.81[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs1901166	0.88[EUR][1000 genomes]
rs2122569	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2250856	0.93[EUR][1000 genomes]
rs2443035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2443040	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2455301	0.93[EUR][1000 genomes]
rs2455302	0.91[EUR][1000 genomes]
rs2455305	0.88[YRI][hapmap]
rs2455309	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2455311	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2455312	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2455314	0.91[EUR][1000 genomes]
rs2459463	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2459465	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2459467	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2597738	0.93[EUR][1000 genomes]
rs2597739	0.93[EUR][1000 genomes]
rs2597746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs323565	0.84[CHD][hapmap];0.86[JPT][hapmap]
rs324063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324066	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324067	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs324068	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs324072	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35642126	0.93[EUR][1000 genomes]
rs364443	0.82[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs420220	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs438652	0.81[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs6861054	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6876739	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6887212	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6895963	0.93[EUR][1000 genomes]
rs837383	0.82[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	nsv881467	chr5:40869802-41008650	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv2757114	chr5:40874078-41009282	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv2759341	chr5:40874078-41009282	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv823055	chr5:40875708-41004839	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv35077	chr5:40875843-41000671	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv830268	chr5:40897361-41138366	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1376178	C5orf34	cis	parietal	SCAN
rs1376178	DAB2	cis	cerebellum	SCAN
rs1376178	RPL37	Cis_1M	lymphoblastoid	RTeQTL
rs1376178	OXCT1	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40904600-40909600	Weak transcription	Colon Smooth Muscle	Colon
2	chr5:40905200-40909000	Weak transcription	Fetal Kidney	kidney
3	chr5:40905400-40909200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr5:40905400-40909200	Weak transcription	Stomach Mucosa	stomach
5	chr5:40905400-40915000	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr5:40905600-40909200	Weak transcription	Duodenum Mucosa	Duodenum
7	chr5:40905600-40909400	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr5:40905600-40909800	Weak transcription	Liver	Liver
9	chr5:40905600-40915000	Weak transcription	Gastric	stomach
10	chr5:40906000-40909200	Weak transcription	Fetal Heart	heart
11	chr5:40906600-40909400	Weak transcription	Ovary	ovary
12	chr5:40906600-40909400	Weak transcription	Pancreas	Pancrea
13	chr5:40906800-40909400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr5:40907000-40909400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr5:40907000-40909400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr5:40908200-40909200	Enhancers	Fetal Lung	lung
17	chr5:40908600-40909400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr5:40908800-40909200	Enhancers	Fetal Intestine Large	intestine
19	chr5:40908800-40910000	Enhancers	Pancreatic Islets	Pancreatic Islet
20	chr5:40908800-40910600	Enhancers	HepG2	liver
21	chr5:40908800-40910800	Enhancers	Fetal Intestine Small	intestine
22	chr5:40908800-40916000	Active TSS	Stomach Smooth Muscle	stomach

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