Variant report

Variant	rs6841454
Chromosome Location	chr4:142635042-142635043
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	FOSL1	chr4:142634830-142635736	HCT-116	colon:	n/a	n/a
2	FOS	chr4:142634913-142635580	MCF10A-Er-Src	breast:	n/a	n/a
3	FOSL2	chr4:142634924-142635693	SK-N-SH	brain:	n/a	n/a
4	EGR1	chr4:142634996-142635679	HCT-116	colon:	n/a	n/a
5	RCOR1	chr4:142634268-142635693	IMR90	lung:	n/a	n/a
6	JUND	chr4:142634956-142635682	SK-N-SH	brain:	n/a	n/a
7	JUND	chr4:142634774-142635683	HCT-116	colon:	n/a	n/a
8	SP1	chr4:142634719-142635723	HCT-116	colon:	n/a	n/a
9	TCF12	chr4:142634807-142635724	SK-N-SH	brain:	n/a	n/a
10	EGR1	chr4:142634950-142635752	HCT-116	colon:	n/a	n/a
11	FOS	chr4:142634988-142635548	MCF10A-Er-Src	breast:	n/a	n/a
12	JUND	chr4:142634944-142635540	Hela-S3	cervix:	n/a	n/a
13	JUND	chr4:142634757-142635760	SK-N-SH	brain:	n/a	n/a
14	FOSL1	chr4:142634783-142635728	HCT-116	colon:	n/a	n/a
15	FOS	chr4:142634964-142635580	MCF10A-Er-Src	breast:	n/a	n/a
16	SP1	chr4:142634748-142635729	HCT-116	colon:	n/a	n/a
17	FOSL2	chr4:142634847-142635655	A549	lung:	n/a	n/a
18	FOS	chr4:142634956-142635580	MCF10A-Er-Src	breast:	n/a	n/a
19	JUND	chr4:142634813-142635655	HCT-116	colon:	n/a	n/a
20	FOS	chr4:142634990-142635614	HUVEC	blood vessel:	n/a	n/a

Variant related genes	Relation type
IL15	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10010469	1.00[ASN][1000 genomes]
rs10028670	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1040257	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11100724	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12508955	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13111860	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1493024	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1500835	1.00[ASN][1000 genomes]
rs1519552	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs1519553	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1589241	0.95[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs1607592	0.89[EUR][1000 genomes]
rs1607593	0.89[EUR][1000 genomes]
rs1850853	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2087849	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2254514	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2322262	1.00[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs4055041	1.00[ASN][1000 genomes]
rs4956305	1.00[ASN][1000 genomes]
rs4956404	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4956405	0.83[GIH][hapmap]
rs4956407	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6537058	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs6816210	0.90[CEU][hapmap]
rs6837991	0.95[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs6850492	0.83[GIH][hapmap]
rs7661408	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7688250	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7698675	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs937177	1.00[ASN][1000 genomes]
rs970328	0.81[EUR][1000 genomes]
rs990851	0.95[CEU][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880173	chr4:142355535-142666106	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv3401979	chr4:142434442-142803321	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1018949	chr4:142451823-142732365	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1030822	chr4:142487721-142706053	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1027004	chr4:142487721-143007320	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	esv3448093	chr4:142612197-142704695	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6841454	MED9	trans	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:142608800-142655000	Weak transcription	Gastric	stomach
2	chr4:142624000-142652000	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr4:142624200-142651000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr4:142629400-142651000	Weak transcription	Left Ventricle	heart
5	chr4:142629400-142654600	Weak transcription	Esophagus	oesophagus
6	chr4:142629400-142655000	Weak transcription	Spleen	Spleen
7	chr4:142629600-142635200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr4:142629600-142637600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr4:142629600-142657600	Weak transcription	Right Ventricle	heart
10	chr4:142629800-142637400	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr4:142630000-142638600	Weak transcription	Aorta	Aorta
12	chr4:142630000-142650400	Weak transcription	Primary B cells from peripheral blood	blood
13	chr4:142630200-142637800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr4:142631800-142637600	Weak transcription	GM12878-XiMat	blood
15	chr4:142633400-142635200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr4:142634200-142636200	Enhancers	Hela-S3	cervix
17	chr4:142634400-142635800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr4:142634400-142635800	Enhancers	NHLF	lung
19	chr4:142634400-142636000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr4:142634600-142635200	Enhancers	Muscle Satellite Cultured Cells	--
21	chr4:142634600-142635600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr4:142634600-142635800	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr4:142634600-142635800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr4:142634600-142635800	Enhancers	HSMM	muscle
25	chr4:142634600-142635800	Enhancers	HSMMtube	muscle
26	chr4:142634600-142635800	Enhancers	NHDF-Ad	bronchial
27	chr4:142634600-142635800	Enhancers	NHEK	skin
28	chr4:142634600-142635800	Enhancers	Osteobl	bone
29	chr4:142634600-142636000	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr4:142634600-142636000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr4:142634600-142636000	Enhancers	HMEC	breast
32	chr4:142634600-142636200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr4:142634600-142653600	Weak transcription	Colon Smooth Muscle	Colon
34	chr4:142634800-142635600	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr4:142634800-142635600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr4:142634800-142635800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr4:142634800-142636000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr4:142634800-142636000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr4:142634800-142641600	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr4:142634800-142656200	Weak transcription	Pancreas	Pancrea
41	chr4:142635000-142635600	Flanking Active TSS	NH-A	brain
42	chr4:142635000-142635800	Enhancers	H9 Cell Line	embryonic stem cell
43	chr4:142635000-142635800	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr4:142635000-142635800	Enhancers	HUVEC	blood vessel
45	chr4:142635000-142636200	Enhancers	A549	lung

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