Variant report

Variant	rs7546569
Chromosome Location	chr1:228802765-228802766
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10916348	1.00[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10916349	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12040713	0.84[ASN][1000 genomes]
rs12046644	0.95[CHB][hapmap];0.86[CHD][hapmap];0.81[MEX][hapmap]
rs12047219	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12060147	0.92[EUR][1000 genomes]
rs1925715	0.89[CHB][hapmap];0.81[MEX][hapmap]
rs4344301	0.89[CHB][hapmap]
rs6658934	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6661618	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6672815	0.90[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6681216	0.93[CHB][hapmap];0.88[JPT][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7355046	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7355153	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv1013500	chr1:228459134-228849601	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv1013051	chr1:228786702-228903706	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv997801	chr1:228786702-228975127	Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv870365	chr1:228788356-229267904	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv1009511	chr1:228791784-228853665	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	esv2762224	chr1:228791784-228867656	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv998255	chr1:228791784-228919202	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
9	nsv549299	chr1:228793246-229455876	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7546569	FAM177B	cis	parietal	SCAN
rs7546569	TP53BP2	cis	cerebellum	SCAN
rs7546569	CABC1	cis	parietal	SCAN
rs7546569	SNORD115-33	trans	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228784200-228803000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:228787600-228804600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:228799800-228803400	Enhancers	Placenta	Placenta
4	chr1:228800000-228804400	Weak transcription	Right Atrium	heart
5	chr1:228800200-228804800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:228800200-228805800	Weak transcription	Aorta	Aorta
7	chr1:228800600-228804000	Weak transcription	Brain Substantia Nigra	brain
8	chr1:228800600-228804600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr1:228800800-228804200	Weak transcription	HepG2	liver
10	chr1:228801200-228802800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr1:228802400-228803000	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr1:228802400-228803000	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr1:228802400-228803200	Enhancers	H9 Cell Line	embryonic stem cell
14	chr1:228802400-228803200	Enhancers	Fetal Muscle Leg	muscle
15	chr1:228802400-228803400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:228802400-228803400	Enhancers	Fetal Intestine Large	intestine
17	chr1:228802400-228803400	Enhancers	Fetal Intestine Small	intestine
18	chr1:228802600-228802800	Enhancers	Stomach Mucosa	stomach

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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