Variant report

Variant	rs6540547
Chromosome Location	chr1:209850020-209850021
allele	C/G
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	TBL1XR1	chr1:209850000-209850088	K562	blood:	n/a	n/a
2	JUN	chr1:209845877-209850984	K562	blood:	n/a	chr1:209846829-209846839 chr1:209846830-209846838 chr1:209850154-209850163 chr1:209846657-209846666 chr1:209846828-209846840 chr1:209850457-209850468 chr1:209847133-209847144
3	POLR2A	chr1:209845589-209851436	K562	blood:	n/a	n/a
4	MYC	chr1:209846187-209850023	K562	blood:	n/a	chr1:209846852-209846861 chr1:209846850-209846863 chr1:209846852-209846861 chr1:209846851-209846862 chr1:209846850-209846863 chr1:209846852-209846861 chr1:209846851-209846862 chr1:209846851-209846860
5	JUND	chr1:209849899-209850188	K562	blood:	n/a	chr1:209850154-209850163
6	MAFK	chr1:209850011-209850133	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:209849832..209852641-chr1:209858300..209861222,2	K562	blood:
2	chr1:209811179..209812712-chr1:209849579..209852575,2	K562	blood:

Variant related genes	Relation type
ENSG00000227591	TF binding region
ENSG00000117594	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10082248	1.00[CEU][hapmap]
rs10863780	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12097611	1.00[AFR][1000 genomes]
rs12561766	1.00[CEU][hapmap]
rs17015078	1.00[CEU][hapmap]
rs1883442	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2038053	1.00[CEU][hapmap]
rs2236902	1.00[CEU][hapmap]
rs2272866	1.00[CEU][hapmap]
rs2282740	1.00[CEU][hapmap]
rs2298930	1.00[CEU][hapmap]
rs3820161	1.00[AFR][1000 genomes]
rs4329516	1.00[CEU][hapmap]
rs4393158	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4545339	1.00[CEU][hapmap]
rs4844487	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs4844893	1.00[CEU][hapmap]
rs4844894	1.00[CEU][hapmap]
rs6694238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs701950	0.86[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes]
rs7528642	1.00[CEU][hapmap]
rs846908	1.00[CEU][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs860184	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs932375	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9919217	1.00[AFR][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	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209847400-209850600	Flanking Active TSS	Liver	Liver
2	chr1:209847800-209850200	Active TSS	Psoas Muscle	Psoas
3	chr1:209848400-209850200	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr1:209848400-209850200	Active TSS	Fetal Intestine Large	intestine
5	chr1:209848400-209850600	Active TSS	Right Atrium	heart
6	chr1:209848400-209851600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:209848800-209850800	Bivalent/Poised TSS	Primary B cells from cord blood	blood
8	chr1:209849600-209850200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:209849600-209850400	Enhancers	Colonic Mucosa	Colon
10	chr1:209849600-209850600	Bivalent/Poised TSS	Primary hematopoietic stem cells	blood
11	chr1:209849600-209850600	Bivalent Enhancer	Fetal Muscle Leg	muscle
12	chr1:209849600-209861400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:209849800-209850200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:209849800-209850200	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
15	chr1:209849800-209850200	Bivalent Enhancer	Fetal Kidney	kidney
16	chr1:209849800-209850200	Enhancers	Fetal Stomach	stomach
17	chr1:209849800-209850400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr1:209849800-209850600	Bivalent/Poised TSS	Monocytes-CD14+_RO01746	blood
19	chr1:209849800-209850800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr1:209849800-209850800	Transcr. at gene 5' and 3'	Fetal Lung	lung
21	chr1:209849800-209850800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr1:209849800-209862000	Weak transcription	NHLF	lung
23	chr1:209850000-209850200	Enhancers	Duodenum Mucosa	Duodenum
24	chr1:209850000-209850200	Enhancers	Stomach Smooth Muscle	stomach
25	chr1:209850000-209850600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
26	chr1:209850000-209850600	Active TSS	Skeletal Muscle Male	skeletal muscle
27	chr1:209850000-209851000	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
28	chr1:209850000-209851000	Enhancers	Colon Smooth Muscle	Colon
29	chr1:209850000-209851000	Enhancers	Fetal Heart	heart
30	chr1:209850000-209851400	Active TSS	Adipose Nuclei	Adipose
31	chr1:209850000-209857600	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr1:209850000-209858400	Weak transcription	Ovary	ovary
33	chr1:209850000-209859200	Weak transcription	Left Ventricle	heart

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