Variant report

Variant	rs12401721
Chromosome Location	chr1:95096970-95096971
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11165187	0.85[ASN][1000 genomes]
rs11577320	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11580343	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12123422	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12402912	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12725598	0.82[ASW][hapmap];0.88[GIH][hapmap];0.81[LWK][hapmap];0.86[MKK][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12725602	0.82[ASW][hapmap];0.86[GIH][hapmap];0.86[LWK][hapmap];0.84[MEX][hapmap];0.87[MKK][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12726870	0.81[AFR][1000 genomes]
rs2211318	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4847324	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72729576	0.83[ASN][1000 genomes]
rs9645363	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	nsv1001587	chr1:95027691-95318680	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
2	nsv519997	chr1:95083836-95113417	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1001230	chr1:95085184-95108531	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12401721	GCLM	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:95089800-95100000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr1:95089800-95100400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr1:95090000-95102800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:95090200-95099600	Weak transcription	Fetal Stomach	stomach
5	chr1:95090800-95100600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:95091600-95100400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr1:95095400-95099000	Weak transcription	Pancreas	Pancrea
8	chr1:95095400-95100600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr1:95095400-95100600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:95095400-95100600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:95095800-95098600	Weak transcription	Ovary	ovary
12	chr1:95095800-95099400	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr1:95095800-95101400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr1:95095800-95102200	Weak transcription	Fetal Intestine Small	intestine
15	chr1:95095800-95108400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:95096000-95098400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr1:95096000-95100400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:95096600-95100600	Weak transcription	Placenta	Placenta

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Input of quick search could be:

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

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