Variant report

Variant	rs6540742
Chromosome Location	chr1:212670865-212670866
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212670285..212672313-chr1:212782929..212785774,2	K562	blood:
2	chr1:212666396..212668069-chr1:212669745..212672700,2	MCF-7	breast:
3	chr1:212657352..212659830-chr1:212670221..212673074,2	K562	blood:
4	chr1:212670700..212673615-chr1:212795824..212798089,2	K562	blood:
5	chr1:212665451..212668027-chr1:212669826..212672664,2	K562	blood:
6	chr1:212667460..212673417-chr1:212776098..212784429,11	K562	blood:
7	chr1:212670746..212672683-chr1:212733125..212734851,2	K562	blood:

No data

No data

No data

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10779580	0.89[GIH][hapmap];0.96[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs12141407	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12741983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001262	0.83[ASN][1000 genomes]
rs4951604	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs557252	0.82[ASN][1000 genomes]
rs572235	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs590156	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs611108	0.89[GIH][hapmap]
rs626178	0.85[CHD][hapmap];0.83[ASN][1000 genomes]
rs6540743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6681329	1.00[YRI][hapmap]
rs6694514	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs748517	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7515863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7537826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7544479	0.89[GIH][hapmap];0.83[LWK][hapmap];0.81[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised 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 miRNA target site	114 gene(s)	inside rSNPs	diseases
3	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
4	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
5	nsv873160	chr1:212610755-212675482	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv873161	chr1:212610755-212683565	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv873162	chr1:212610755-212716033	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv527863	chr1:212617423-212700618	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	esv2757770	chr1:212648143-212843103	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
10	esv2758996	chr1:212648143-212843103	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
11	esv3329320	chr1:212670772-212671369	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6540742	TMEM206	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212662600-212671200	Weak transcription	Left Ventricle	heart
2	chr1:212662800-212671800	Weak transcription	Lung	lung
3	chr1:212663000-212671400	Weak transcription	Right Atrium	heart
4	chr1:212663200-212678400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:212663400-212671600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr1:212667200-212672000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:212667200-212686400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:212669000-212672400	Enhancers	GM12878-XiMat	blood
9	chr1:212669800-212671400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:212669800-212672000	Weak transcription	Stomach Mucosa	stomach
11	chr1:212669800-212672200	Bivalent Enhancer	HepG2	liver
12	chr1:212670000-212671400	Weak transcription	Brain Angular Gyrus	brain
13	chr1:212670000-212679800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr1:212670200-212672000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:212670400-212671400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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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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